pmid:32111039

Proteomic Analysis of Mucopolysaccharidosis IIIB Mouse Brain.

Valeria De Pasquale · Michele Costanzo · Rosa Anna Siciliano · Maria Fiorella Mazzeo · Valeria Pistorio · Laura Bianchi · Emanuela Marchese · Margherita Ruoppolo · Luigi Michele Pavone · Marianna Caterino

Biomolecules · 2020 doi:10.3390/biom10030355

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.

In this file

The fields below come from the published .science file. Expand a section to inspect its evidence.

Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator

sci_version

1.2

pmid:32111039

kind

science-record

revision

content_hash

sha256:dbc510da81c6e10a7fe806aa4dcc343fc1cdc9d0701f3f39982a861b69ca7d32

schema

https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json

created_at

2026-11-01T15:40:57Z

updated_at

2026-11-01T22:01:20Z

generator object · 2 fields

name

corpus-assay-engine

run_id

reading-sci-2026-11-01

paper object · 10 fields

state

complete

title

Proteomic Analysis of Mucopolysaccharidosis IIIB Mouse Brain.

doi

10.3390/biom10030355

pmid

32111039

authors array · 10 items

[0]

Valeria De Pasquale

[1]

Michele Costanzo

[2]

Rosa Anna Siciliano

[3]

Maria Fiorella Mazzeo

[4]

Valeria Pistorio

[5]

Laura Bianchi

[6]

Emanuela Marchese

[7]

Margherita Ruoppolo

[8]

Luigi Michele Pavone

[9]

Marianna Caterino

journal

Biomolecules

year

2020

abstract

Mucopolysaccharidosis IIIB (MPS IIIB) is an inherited metabolic disease due to deficiency of α-N-Acetylglucosaminidase (NAGLU) enzyme with subsequent storage of undegraded heparan sulfate (HS). The main clinical manifestations of the disease are profound intellectual disability and neurodegeneration. A label-free quantitative proteomic approach was applied to compare the proteome profile of brains from MPS IIIB and control mice to identify altered neuropathological pathways of MPS IIIB. Proteins were identified through a bottom up analysis and 130 were significantly under-represented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple bioinformatic analyses allowed to identify three major clusters of the differentially abundant proteins: proteins involved in cytoskeletal regulation, synaptic vesicle trafficking, and energy metabolism. The proteome profile of NAGLU-/- mouse brain could pave the way for further studies aimed at identifying novel therapeutic targets for the MPS IIIB. Data are available via ProteomeXchange with the identifier PXD017363.

claims array · 2 items

[0] object · 6 fields

claim-method

statement

A Student’s t test was used to select proteins showing significant changes between the analyzed datasets, resulting in two-tailed p values.

kind

methodological

target

null

evidence array · 1 item

[0] object · 3 fields

asset

source:pmid:32111039

locator

sections[7] "2.5. Quantitative Label-Free Proteomic Analysis" paragraph 2

quote

A Student’s t test was used to select proteins showing significant changes between the analyzed datasets, resulting in two-tailed p values.

state

complete

[1] object · 6 fields

claim-data-access

statement

Data are available via ProteomeXchange with the identifier PXD017363.

kind

methodological

target

null

evidence array · 1 item

[0] object · 3 fields

asset

source:pmid:32111039

locator

sections[0] "Abstract" paragraph 1

quote

Data are available via ProteomeXchange with the identifier PXD017363.

state

complete

gaps array · 0 items

experiment object · 8 fields

state

partial

objective

null

steps array · 3 items

[0] object · 13 fields

read_published_estimate

order

name

Read the published estimate from the source

kind

other

state

complete

blocked_on

null

description

The claim, method and evidence span published with the source article.

duration_hours

null

parameters object · 0 fields

inputs array · 1 item

[0]

source:pmid:32111039

outputs array · 1 item

[0]

the published estimate and its evidence

instruments array · 0 items

reagents array · 0 items

[1] object · 13 fields

obtain_source_data

order

name

Obtain the source data from the named repository

kind

data-preparation

state

blocked

blocked_on

data:accession_absent

description

The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.

duration_hours

null

parameters object · 0 fields

inputs array · 0 items

outputs array · 1 item

[0]

the source data with its repository provenance

instruments array · 0 items

reagents array · 0 items

[2] object · 13 fields

run_analysis

order

name

Run the published analysis

kind

analysis

state

complete

blocked_on

null

description

Apply the paper's statistical method to the resolved series and compare the result with the published target.

duration_hours

null

parameters object · 0 fields

inputs array · 0 items

outputs array · 1 item

[0]

the replicated result and its comparison

instruments array · 0 items

reagents array · 0 items

materials array · 0 items

instruments array · 0 items

reagents array · 0 items

conditions object · 0 fields

gaps array · 1 item

[0]

step:obtain_source_data blocked on data:accession_absent

data object · 3 fields

state

partial

assets array · 3 items

[0] object · 15 fields

source:pmid:32111039

role

manuscript

format

xml

media_type

application/xml

uri

https://doi.org/10.3390/biom10030355

sha256

sha256:115419db70cdfbfefba1b434eaddf9cd73da450f260b753669d019a76bc11fd4

bytes

67353

access

open

state

resolved

reader

null

reader_status

reader_required

identifier

10.3390/biom10030355

version

null

note

Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.

structure object · 4 fields

pmcid

PMC7175334

source

europe_pmc_fulltext

coverage

whole_body

text_hash_scope

rendered_section_body

[1] object · 16 fields

asset:table:pmid:32111039:1

role

table

format

jats-table

media_type

application/vnd.jats.table+json

uri

null

sha256

sha256:6b91a3940dd2979cb8cf356268b25a0869b26262a5fa0a48f64cca1838813e53

bytes

16535

access

open

state

verified

reader

read_table

reader_status

available

identifier

section[12]/table-wrap[1]#biomolecules-10-00355-t001

version

null

note

Dysregulated proteins in NAGLU−/− mouse brains compared to WT.

structure object · 5 fields

pmcid

PMC7175334

section_index

section_title

3.2. Quantitative Analysis of Differentially Expressed Proteins in Brain Samples from MPS IIIB and WT Mice

row_count

205

column_count

table object · 8 fields

label

Table 1

caption

Dysregulated proteins in NAGLU−/− mouse brains compared to WT.

rows array · 205 items

[0] array · 6 items

[0]

Swiss-Prot Code

[1]

Gene Name

[2]

Protein Description

[3]

Fold NSAF

[4]

p Value

[5]

Subcellular Localization

[1] array · 6 items

[0]

Q545B6

[1]

Stmn1

[2]

Stathmin

[3]

−12.6

[4]

0.00002

[5]

[2] array · 6 items

[0]

Q9QYX7

[1]

Pclo

[2]

Protein piccolo

[3]

−8.4

[4]

0.00101

[5]

CK, GA

[3] array · 6 items

[0]

Q6P9K8

[1]

Caskin1

[2]

Caskin-1

[3]

−3.8

[4]

0.00262

[5]

[4] array · 6 items

[0]

A8DUK2

[1]

Hbbt1

[2]

Beta-globin

[3]

−3.4

[4]

0.00008

[5]

[5] array · 6 items

[0]

Q4VAE3

[1]

Tmem65

[2]

Transmembrane protein 65

[3]

−3.3

[4]

0.00374

[5]

M, PM

[6] array · 6 items

[0]

Q8CHF1

[1]

mKIAA0531

[2]

Kinesin-like protein (Fragment)

[3]

−3.2

[4]

0.00232

[5]

[7] array · 6 items

[0]

P17563

[1]

Selenbp1

[2]

Selenium-binding protein 1

[3]

−3.2

[4]

0.00046

[5]

CK, N

[8] array · 6 items

[0]

Q4KMM3

[1]

Oxr1

[2]

Oxidation resistance protein 1

[3]

−3

[4]

0.00036

[5]

M, N

[9] array · 6 items

[0]

A2AS98

[1]

Nckap1

[2]

Nck-associated protein 1

[3]

−2.9

[4]

0.00209

[5]

CK, PM

[10] array · 6 items

[0]

C7G3P1

[1]

Ppfia3

[2]

MKIAA0654 protein (Fragment)

[3]

−2.6

[4]

0.00328

[5]

[11] array · 6 items

[0]

Q8BVQ5

[1]

Ppme1

[2]

Protein phosphatase methylesterase 1

[3]

−2.5

[4]

0.00345

[5]

[12] array · 6 items

[0]

Q3UVN5

[1]

Nsfl1c

[2]

Putative uncharacterized protein

[3]

−2.5

[4]

0.00002

[5]

CK, GA, N

[13] array · 6 items

[0]

Q9R0Q6

[1]

Arpc1a

[2]

Actin-related protein 2/3 complex subunit 1A

[3]

−2.4

[4]

0.00036

[5]

CK, N, PM

[14] array · 6 items

[0]

Q3TF14

[1]

Ahcy

[2]

Adenosylhomocysteinase

[3]

−2.4

[4]

0.00329

[5]

CK, N

[15] array · 6 items

[0]

Q9CX86

[1]

Hnrnpa0

[2]

Heterogeneous nuclear ribonucleoprotein A0

[3]

−2.4

[4]

0.00165

[5]

[16] array · 6 items

[0]

Q9Z1B3

[1]

Plcb1

[2]

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1

[3]

−2.4

[4]

0.00671

[5]

CK, N, PM

[17] array · 6 items

[0]

O54991

[1]

Cntnap1

[2]

Contactin-associated protein 1

[3]

−2.3

[4]

0.00626

[5]

[18] array · 6 items

[0]

B0V2P5

[1]

Dmxl2

[2]

DmX-like protein 2

[3]

−2.3

[4]

0.01109

[5]

[19] array · 6 items

[0]

E9Q8N8

[1]

Slc4a4

[2]

Anion exchange protein

[3]

−2.3

[4]

0.0011

[5]

[20] array · 6 items

[0]

B1AQX9

[1]

Srcin1

[2]

SRC kinase-signaling inhibitor 1

[3]

−2.3

[4]

0.0004

[5]

[21] array · 6 items

[0]

P24472

[1]

Gsta4

[2]

Glutathione S-transferase A4

[3]

−2.3

[4]

0.00125

[5]

[22] array · 6 items

[0]

Q3UK83

[1]

Hnrnpa1

[2]

Putative uncharacterized protein

[3]

−2.2

[4]

0.00047

[5]

ERS, N

[23] array · 6 items

[0]

D3Z4J3

[1]

Myo5a

[2]

Unconventional myosin-Va

[3]

−2.2

[4]

0.00636

[5]

CK, C, ER, En, GA, Ly, Pe

[24] array · 6 items

[0]

Q61411

[1]

Hras

[2]

GTPase HRas

[3]

−2.2

[4]

0.00583

[5]

C, GA, N, PM

[25] array · 6 items

[0]

Q9Z0X1

[1]

Aifm1

[2]

Apoptosis-inducing factor 1, mitochondrial

[3]

−2.1

[4]

0.00398

[5]

CK, M, N

[26] array · 6 items

[0]

B2L107

[1]

Vsnl1

[2]

Visinin-like protein 1

[3]

−2.1

[4]

0.00018

[5]

[27] array · 6 items

[0]

Q9DBF1

[1]

Aldh7a

[2]

Alpha-aminoadipic semialdehyde dehydrogenase

[3]

−2.1

[4]

0.02264

[5]

C, M, N

[28] array · 6 items

[0]

Q3TJF2

[1]

Ola1

[2]

Obg-like ATPase 1

[3]

−2.1

[4]

0.00001

[5]

CK, C, N

[29] array · 6 items

[0]

Q8VDD5

[1]

Myh9

[2]

Myosin-9

[3]

−2

[4]

0.01358

[5]

C, CK, N, PM

[30] array · 6 items

[0]

Q9JJK2

[1]

Lancl2

[2]

LanC-like protein 2

[3]

−2

[4]

0.00232

[5]

C, CK, N, PM

[31] array · 6 items

[0]

E9Q2L2

[1]

Dlg2

[2]

Disks large homolog 2

[3]

−2

[4]

0.00218

[5]

[32] array · 6 items

[0]

Q91VR5

[1]

Ddx1

[2]

ATP-dependent RNA helicase DDX1

[3]

−2

[4]

0.00216

[5]

C, M, N

[33] array · 6 items

[0]

Q9JHU4

[1]

Dync1h1

[2]

Cytoplasmic dynein 1 heavy chain 1

[3]

−2

[4]

0.00407

[5]

CK, N

[34] array · 6 items

[0]

Q99PU5

[1]

Acsbg1

[2]

Long-chain-fatty-acid--CoA ligase ACSBG1

[3]

−1.9

[4]

0.01942

[5]

ER, PM

[35] array · 6 items

[0]

Q64010

[1]

Crk

[2]

Adapter molecule crk

[3]

−1.9

[4]

0.0031

[5]

CK, PM

[36] array · 6 items

[0]

P14733

[1]

Lmnb1

[2]

Lamin-B1

[3]

−1.9

[4]

0.02293

[5]

CK, N

[37] array · 6 items

[0]

P54775

[1]

Psmc4

[2]

26S protease regulatory subunit 6B

[3]

−1.9

[4]

0.03099

[5]

CK, N

[38] array · 6 items

[0]

A0A1S6GWI0

[1]

Ndufa8

[2]

NADH dehydrogenase (Ubiquinone) 1 alpha subcomplex, 8

[3]

−1.8

[4]

0.00156

[5]

[39] array · 6 items

[0]

Q3U741

[1]

Ddx17

[2]

DEAD (Asp-Glu-Ala-Asp) box polypeptide 17, isoform CRA_a

[3]

−1.8

[4]

0.00085

[5]

C, N

[40] array · 6 items

[0]

Q3TIQ2

[1]

Rpl12

[2]

Putative uncharacterized protein

[3]

−1.8

[4]

0.01139

[5]

C, N

[41] array · 6 items

[0]

P70168

[1]

Kpnb1

[2]

Importin subunit beta-1

[3]

−1.7

[4]

0.00011

[5]

C, M, N

[42] array · 6 items

[0]

Q80TZ3

[1]

Dnajc6

[2]

Putative tyrosine-protein phosphatase auxilin

[3]

−1.7

[4]

0.00164

[5]

[43] array · 6 items

[0]

Q5DTG0

[1]

Atp8a1

[2]

Phospholipid-transporting ATPase (Fragment)

[3]

−1.7

[4]

0.00428

[5]

ER, GA, PM

[44] array · 6 items

[0]

Q9QXS1

[1]

Plec

[2]

Plectin

[3]

−1.7

[4]

0.00377

[5]

C, CK, PM

[45] array · 6 items

[0]

Q921F2

[1]

Tardbp

[2]

TAR DNA-binding protein 43

[3]

−1.7

[4]

0.00786

[5]

[46] array · 6 items

[0]

B2RX08

[1]

Sptb

[2]

Spectrin beta chain

[3]

−1.7

[4]

0.00319

[5]

C, CK, PM

[47] array · 6 items

[0]

Q3TKG4

[1]

Psmc3

[2]

Putative uncharacterized protein (Fragment)

[3]

−1.6

[4]

0.00396

[5]

[48] array · 6 items

[0]

Q3UH59

[1]

Myh10

[2]

Myosin-10

[3]

−1.6

[4]

0.02527

[5]

C, CK, PM

[49] array · 6 items

[0]

Q9JM76

[1]

Arpc3

[2]

Actin-related protein 2/3 complex subunit 3

[3]

−1.6

[4]

0.01437

[5]

C, N

[50] array · 5 items

[0]

A0A1S6GWJ8

[1]

Uncharacterized protein

[2]

–1,5

[3]

0.02713

[4]

[51] array · 6 items

[0]

Q3UN60

[1]

Mpp6

[2]

Membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6), isoform CRA_b

[3]

−1.5

[4]

0.00085

[5]

[52] array · 6 items

[0]

Q91XV3

[1]

Basp1

[2]

Brain acid soluble protein 1

[3]

−1.5

[4]

0.00001

[5]

N, PM

[53] array · 6 items

[0]

Q07076

[1]

Anxa7

[2]

Annexin A7

[3]

−1.5

[4]

0.01183

[5]

C, ER, ERS, N, PM

[54] array · 6 items

[0]

Q3UY05

[1]

Ndufs8

[2]

Putative uncharacterized protein

[3]

−1.4

[4]

0.00008

[5]

[55] array · 6 items

[0]

A0A0R4J0Q5

[1]

Lmnb2

[2]

Lamin-B2

[3]

−1.4

[4]

0.03275

[5]

CK, N

[56] array · 6 items

[0]

Q4FJX9

[1]

Sod2

[2]

Superoxide dismutase

[3]

−1.4

[4]

0.01379

[5]

[57] array · 6 items

[0]

Q91VN4

[1]

Chchd6

[2]

MICOS complex subunit Mic25

[3]

−1.4

[4]

0.01573

[5]

C, M

[58] array · 6 items

[0]

O88737

[1]

Bsn

[2]

Protein bassoon

[3]

−1.3

[4]

0.00915

[5]

C, GA

[59] array · 6 items

[0]

Q3UWW9

[1]

Psmd11

[2]

Putative uncharacterized protein

[3]

−1.3

[4]

0.01386

[5]

C, N

[60] array · 6 items

[0]

O08788

[1]

Dctn1

[2]

Dynactin subunit 1

[3]

−1.3

[4]

0.01243

[5]

CK, C, ERS, N

[61] array · 6 items

[0]

A0A0R4J275

[1]

Ndufa12

[2]

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

[3]

−1.3

[4]

0.0197

[5]

C, M

[62] array · 6 items

[0]

Q63932

[1]

Map2k2

[2]

Dual specificity mitogen-activated protein kinase kinase 2

[3]

−1.3

[4]

0.01951

[5]

CK, C, ER, En, GA, M, N, PM

[63] array · 6 items

[0]

Q61361

[1]

Bcan

[2]

Brevican core protein

[3]

−1.3

[4]

0.01264

[5]

ERS

[64] array · 6 items

[0]

Q3V117

[1]

Acly

[2]

ATP-citrate synthase

[3]

−1.3

[4]

0.0078

[5]

C, M, N, PM

[65] array · 6 items

[0]

Q8R570

[1]

Snap47

[2]

Synaptosomal-associated protein 47

[3]

−1.3

[4]

0.00248

[5]

C, PM

[66] array · 6 items

[0]

Q9DCS9

[1]

Ndufb10

[2]

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

[3]

−1.2

[4]

0.01688

[5]

[67] array · 6 items

[0]

P14824

[1]

Anxa6

[2]

Annexin A6

[3]

−1.2

[4]

0.01378

[5]

C, En, ERS, Ly, M, N, PM

[68] array · 6 items

[0]

P54071

[1]

Idh2

[2]

Isocitrate dehydrogenase [NADP], mitochondrial

[3]

−1.2

[4]

0.00039

[5]

C, M, Pe

[69] array · 6 items

[0]

Q7TSJ2

[1]

Map6

[2]

Microtubule-associated protein 6

[3]

−1.2

[4]

0.00159

[5]

CK, GA

[70] array · 6 items

[0]

Q8BGN3

[1]

Enpp6

[2]

Ectonucleotide pyrophosphatase/phosphodiesterase family member 6

[3]

−1.2

[4]

0.03099

[5]

ERS, PM

[71] array · 6 items

[0]

Q9CZD3

[1]

Gars

[2]

Glycine--tRNA ligase

[3]

−1.2

[4]

0.01474

[5]

C, ERS, M

[72] array · 6 items

[0]

A0A0R4J083

[1]

Acadl

[2]

Long-chain-specific acyl-CoA dehydrogenase, mitochondrial

[3]

−1.2

[4]

0.03611

[5]

[73] array · 6 items

[0]

Q8CGK3

[1]

Lonp1

[2]

Lon protease homolog, mitochondrial

[3]

−1.1

[4]

0.01936

[5]

C, M, N

[74] array · 6 items

[0]

E9Q7Q3

[1]

Tpm3

[2]

Tropomyosin alpha-3 chain

[3]

−1.1

[4]

0.00355

[5]

CK, C

[75] array · 6 items

[0]

Q8BWT1

[1]

Acaa2

[2]

3-ketoacyl-CoA thiolase, mitochondrial

[3]

−1.1

[4]

0.04478

[5]

[76] array · 6 items

[0]

P61226

[1]

Rap2b

[2]

Ras-related protein Rap-2b

[3]

−1.1

[4]

0.03025

[5]

C, En, ERS, PM

[77] array · 6 items

[0]

Q8R5C5

[1]

Actr1b

[2]

Beta-centractin

[3]

−1.1

[4]

0.00172

[5]

[78] array · 6 items

[0]

E9Q0J5

[1]

Kif21a

[2]

Kinesin-like protein KIF21A

[3]

−1.1

[4]

0.04345

[5]

CK, C, PM

[79] array · 6 items

[0]

B9EKR1

[1]

Ptprz1

[2]

Receptor-type tyrosine-protein phosphatase zeta

[3]

−1.1

[4]

0.01214

[5]

ERS, PM

[80] array · 6 items

[0]

Q6ZQ38

[1]

Cand1

[2]

Cullin-associated NEDD8-dissociated protein 1

[3]

−1

[4]

0.00177

[5]

C, GA, N

[81] array · 6 items

[0]

Q9JI91

[1]

Actn2

[2]

Alpha-actinin-2

[3]

−1

[4]

0.00286

[5]

CK, PM

[82] array · 6 items

[0]

P68040

[1]

Rack1

[2]

Receptor of activated protein C kinase 1

[3]

−1

[4]

0.03823

[5]

CK, M, N, PM

[83] array · 6 items

[0]

E9PUL5

[1]

Prrt2

[2]

Proline-rich transmembrane protein 2

[3]

−1

[4]

0.0411

[5]

[84] array · 6 items

[0]

F6SEU4

[1]

Syngap1

[2]

Ras/Rap GTPase-activating protein SynGAP

[3]

−1

[4]

0.03268

[5]

[85] array · 6 items

[0]

Q8CHG1

[1]

Dclk1

[2]

MKIAA0369 protein (Fragment)

[3]

−1

[4]

0.02306

[5]

[86] array · 6 items

[0]

Q61490

[1]

Alcam

[2]

CD166 antigen

[3]

−1

[4]

0.03414

[5]

[87] array · 6 items

[0]

D3Z656

[1]

Synj1

[2]

Synaptojanin-1

[3]

−1

[4]

0.02126

[5]

[88] array · 6 items

[0]

H3BIV5

[1]

Akap5

[2]

A-kinase anchor protein 5

[3]

−1

[4]

0.01709

[5]

CK, PM

[89] array · 6 items

[0]

Q8VD37

[1]

Sgip1

[2]

SH3-containing GRB2-like protein 3-interacting protein 1

[3]

−1

[4]

0.04017

[5]

CK, PM

[90] array · 6 items

[0]

W6PPR4

[1]

Ank3

[2]

480-kDa ankyrinG

[3]

−1

[4]

0.00579

[5]

CK, C, PM

[91] array · 6 items

[0]

Q9CWS0

[1]

Ddah1

[2]

N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

[3]

−0.9

[4]

0.04649

[5]

[92] array · 6 items

[0]

Q11011

[1]

Npepps

[2]

Puromycin-sensitive aminopeptidase

[3]

−0.9

[4]

0.00505

[5]

C, N

[93] array · 6 items

[0]

Q3TXE5

[1]

Canx

[2]

Putative uncharacterized protein

[3]

−0.9

[4]

0.00488

[5]

ER, PM

[94] array · 6 items

[0]

Q3UAG2

[1]

Pgd

[2]

6-phosphogluconate dehydrogenase, decarboxylating

[3]

−0.9

[4]

0.02403

[5]

[95] array · 6 items

[0]

Q99JX6

[1]

Anxa6

[2]

Annexin

[3]

−0.9

[4]

0.04313

[5]

C, En, ERS, Ly, M, N, PM

[96] array · 6 items

[0]

A0A0G2JEG8

[1]

Amph

[2]

Amphiphysin

[3]

−0.9

[4]

0.00912

[5]

CK, PM

[97] array · 6 items

[0]

Q99P72

[1]

Rtn4

[2]

Reticulon-4

[3]

−0.9

[4]

0.01061

[5]

ER, N, PM

[98] array · 6 items

[0]

Q49S98

[1]

Slc32a1

[2]

Putative uncharacterized protein

[3]

−0.9

[4]

0.04098

[5]

[99] array · 6 items

[0]

B2RQQ5

[1]

Map1b

[2]

Microtubule-associated protein 1B

[3]

−0.9

[4]

0.03443

[5]

CK, C, PM

[100] array · 6 items

[0]

D3Z2H9

[1]

Tpm3

[2]

Uncharacterized protein

[3]

−0.9

[4]

0.02982

[5]

CK, C

[101] array · 6 items

[0]

Q6ZQ61

[1]

Matr3

[2]

MCG121979, isoform CRA_c (Fragment)

[3]

−0.8

[4]

0.01811

[5]

[102] array · 6 items

[0]

Q3TE45

[1]

Sdhb

[2]

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

[3]

−0.8

[4]

0.01667

[5]

M, N, PM

[103] array · 6 items

[0]

Q0VF55

[1]

Atp2b3

[2]

Calcium-transporting ATPase

[3]

−0.8

[4]

0.03416

[5]

[104] array · 6 items

[0]

Q3UEG9

[1]

Flot2

[2]

Putative uncharacterized protein

[3]

−0.8

[4]

0.02632

[5]

CK, En, PM

[105] array · 6 items

[0]

Q91V61

[1]

Sfxn3

[2]

Sideroflexin-3

[3]

−0.8

[4]

0.00937

[5]

[106] array · 6 items

[0]

P61164

[1]

Actr1a

[2]

Alpha-centractin

[3]

−0.8

[4]

0.03531

[5]

[107] array · 6 items

[0]

Q571M2

[1]

Hspa4

[2]

MKIAA4025 protein (Fragment)

[3]

−0.7

[4]

0.00487

[5]

C, ERS, N

[108] array · 6 items

[0]

Q9Z2Y3

[1]

Homer1

[2]

Homer protein homolog 1

[3]

−0.7

[4]

0.01584

[5]

C, PM

[109] array · 6 items

[0]

E9Q455

[1]

Tpm1

[2]

Tropomyosin alpha-1 chain

[3]

−0.7

[4]

0.04225

[5]

[110] array · 6 items

[0]

A2A5Y6

[1]

Mapt

[2]

Microtubule-associated protein

[3]

−0.7

[4]

0.04838

[5]

CK, C, N, PM

[111] array · 5 items

[0]

A0A1S6GWH1

[1]

Uncharacterized protein

[2]

–0,7

[3]

0.02404

[4]

[112] array · 6 items

[0]

P35486

[1]

Pdha1

[2]

Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

[3]

−0.6

[4]

0.00552

[5]

M, N

[113] array · 6 items

[0]

Q8CC13

[1]

Ap1b1

[2]

AP complex subunit beta

[3]

−0.6

[4]

0.03216

[5]

C, GA

[114] array · 6 items

[0]

E9Q2W9

[1]

Actn4

[2]

Alpha-actinin-4 (Fragment)

[3]

−0.6

[4]

0.00847

[5]

CK, C, N

[115] array · 6 items

[0]

Q8BVE3

[1]

Atp6v1h

[2]

V-type proton ATPase subunit H

[3]

−0.6

[4]

0.02175

[5]

C, Ly

[116] array · 6 items

[0]

A0A0A6YY91

[1]

Ncam1

[2]

Neural cell adhesion molecule 1 (Fragment)

[3]

−0.6

[4]

0.0182

[5]

CK, PM

[117] array · 6 items

[0]

Q3TYK4

[1]

Prkar1a

[2]

Putative uncharacterized protein

[3]

−0.6

[4]

0.01177

[5]

CK, C, PM

[118] array · 6 items

[0]

P12960

[1]

Cntn1

[2]

Contactin-1

[3]

−0.6

[4]

0.02931

[5]

[119] array · 6 items

[0]

Q3TPZ5

[1]

Dctn2

[2]

Dynactin 2

[3]

−0.6

[4]

0.00054

[5]

CK, C

[120] array · 6 items

[0]

A0A1L1SV25

[1]

Actn4

[2]

Alpha-actinin-4

[3]

−0.6

[4]

0.0286

[5]

CK, C, N

[121] array · 6 items

[0]

P19246

[1]

Nefh

[2]

Neurofilament heavy polypeptide

[3]

−0.5

[4]

0.04106

[5]

CK, M, N, PM

[122] array · 6 items

[0]

A0A0R4J117

[1]

Igsf8

[2]

Immunoglobulin superfamily member 8

[3]

−0.5

[4]

0.04908

[5]

[123] array · 6 items

[0]

Q68FG2

[1]

Sptbn2

[2]

Spectrin beta chain

[3]

−0.5

[4]

0.04372

[5]

CK, C, ER, En, GA

[124] array · 6 items

[0]

Q80YU5

[1]

Mog

[2]

Myelin oligodendrocyte glycoprotein (Fragment)

[3]

−0.5

[4]

0.02477

[5]

C, ER, M, PM

[125] array · 6 items

[0]

E9QB01

[1]

Ncam1

[2]

Neural cell adhesion molecule 1

[3]

−0.5

[4]

0.03648

[5]

C, PM

[126] array · 6 items

[0]

Q01853

[1]

Vcp

[2]

Transitional endoplasmic reticulum ATPase

[3]

−0.5

[4]

0.03249

[5]

C, ER, N

[127] array · 6 items

[0]

P09041

[1]

Pgk2

[2]

Phosphoglycerate kinase 2

[3]

−0.4

[4]

0.03696

[5]

[128] array · 6 items

[0]

Q7TPR4

[1]

Actn1

[2]

Alpha-actinin-1

[3]

−0.4

[4]

0.01557

[5]

CK, N, PM

[129] array · 6 items

[0]

P63011

[1]

Rab3a

[2]

Ras-related protein Rab-3A

[3]

−0.4

[4]

0.0162

[5]

C, En, Ly, PM

[130] array · 6 items

[0]

P09411

[1]

Pgk1

[2]

Phosphoglycerate kinase 1

[3]

−0.3

[4]

0.01617

[5]

C, ERS, PM

[131] array · 6 items

[0]

O08599

[1]

Stxbp1

[2]

Syntaxin-binding protein 1

[3]

0.1

[4]

0.03134

[5]

CK, C, M, PM

[132] array · 6 items

[0]

A0A0A0MQA5

[1]

Tuba4a

[2]

Tubulin alpha chain (Fragment)

[3]

0.2

[4]

0.01472

[5]

[133] array · 6 items

[0]

P68369

[1]

Tuba1a

[2]

Tubulin alpha-1A chain

[3]

0.2

[4]

0.02299

[5]

CK, En

[134] array · 6 items

[0]

Q52L87

[1]

Tuba1c

[2]

Tubulin alpha chain

[3]

0.3

[4]

0.0146

[5]

CK, N

[135] array · 6 items

[0]

P50396

[1]

Gdi1

[2]

Rab GDP dissociation inhibitor alpha

[3]

0.3

[4]

0.03464

[5]

[136] array · 6 items

[0]

P60710

[1]

Actb

[2]

Actin, cytoplasmic 1

[3]

0.3

[4]

0.02793

[5]

CK, C, N, PM

[137] array · 6 items

[0]

Q9CZU6

[1]

[2]

Citrate synthase, mitochondrial

[3]

0.3

[4]

0.00075

[5]

[138] array · 6 items

[0]

P05202

[1]

Got2

[2]

Aspartate aminotransferase, mitochondrial

[3]

0.3

[4]

0.03387

[5]

M, PM

[139] array · 6 items

[0]

P63038

[1]

Hspd1

[2]

60 kDa heat shock protein, mitochondrial

[3]

0.3

[4]

0.02215

[5]

CK, ER, En, ERS, GA, M, PM

[140] array · 6 items

[0]

E9Q912

[1]

Rap1gds1

[2]

RAP1, GTP-GDP dissociation stimulator 1

[3]

0.3

[4]

0.00467

[5]

CK, ER, M

[141] array · 6 items

[0]

B2CSK2

[1]

[2]

Heat shock protein 1-like protein

[3]

0.3

[4]

0.00172

[5]

[142] array · 6 items

[0]

O88935

[1]

Syn1

[2]

Synapsin-1

[3]

0.3

[4]

0.03624

[5]

CK, C, GA, N

[143] array · 6 items

[0]

P68033

[1]

Actc1

[2]

Actin, alpha cardiac muscle 1

[3]

0.3

[4]

0.00986

[5]

[144] array · 6 items

[0]

P08249

[1]

Mdh2

[2]

Malate dehydrogenase, mitochondrial

[3]

0.3

[4]

0.00731

[5]

[145] array · 6 items

[0]

Q03265

[1]

Atp5a1

[2]

ATP synthase subunit alpha, mitochondrial

[3]

0.3

[4]

0.00169

[5]

M, N, PM

[146] array · 6 items

[0]

Q99KI0

[1]

Aco2

[2]

Aconitate hydratase, mitochondrial

[3]

0.3

[4]

0.00087

[5]

C, M

[147] array · 6 items

[0]

P17879

[1]

Hspa1b

[2]

Heat shock 70 kDa protein 1B

[3]

0.4

[4]

0.00362

[5]

CK, C, M, N, PM

[148] array · 6 items

[0]

O08553

[1]

Dpysl2

[2]

Dihydropyrimidinase-related protein 2

[3]

0.4

[4]

0.00004

[5]

CK, C, M, PM

[149] array · 6 items

[0]

Q5FW97

[1]

EG433182

[2]

Enolase 1, alpha non-neuron

[3]

0.4

[4]

0.00346

[5]

[150] array · 6 items

[0]

Q64332

[1]

Syn2

[2]

Synapsin-2

[3]

0.4

[4]

0.01708

[5]

[151] array · 6 items

[0]

Q3TQ70

[1]

Gnb1

[2]

Beta1 subnuit of GTP-binding protein

[3]

0.4

[4]

0.01897

[5]

[152] array · 6 items

[0]

P62631

[1]

Eef1a2

[2]

Elongation factor 1-alpha 2

[3]

0.4

[4]

0.00011

[5]

[153] array · 6 items

[0]

P80316

[1]

Cct5

[2]

T-complex protein 1 subunit epsilon

[3]

0.4

[4]

0.04942

[5]

CK, C

[154] array · 6 items

[0]

Q8CE19

[1]

Syn2

[2]

Putative uncharacterized protein

[3]

0.4

[4]

0.02198

[5]

[155] array · 6 items

[0]

Q3UA81

[1]

Eef1a1

[2]

Elongation factor 1-alpha

[3]

0.4

[4]

0.00003

[5]

CK, C, M, PM

[156] array · 6 items

[0]

Q8C2Q7

[1]

Hnrnph1

[2]

Heterogeneous nuclear ribonucleoprotein H

[3]

0.4

[4]

0.01261

[5]

C, N

[157] array · 6 items

[0]

Q9D6F9

[1]

Tubb4a

[2]

Tubulin beta-4A chain

[3]

0.4

[4]

0.00031

[5]

[158] array · 6 items

[0]

P17751

[1]

Tpi1

[2]

Triosephosphate isomerase

[3]

0.4

[4]

0.00008

[5]

[159] array · 6 items

[0]

P48774

[1]

Gstm5

[2]

Glutathione S-transferase Mu 5

[3]

0.4

[4]

0.01045

[5]

C, ERS

[160] array · 6 items

[0]

P18872

[1]

Gnao1

[2]

Guanine nucleotide-binding protein G(o) subunit alpha

[3]

0.4

[4]

0.00334

[5]

[161] array · 6 items

[0]

Q3UYK6

[1]

Slc1a2

[2]

Amino acid transporter

[3]

0.4

[4]

0.03711

[5]

[162] array · 6 items

[0]

Q8BVI4

[1]

Qdpr

[2]

Dihydropteridine reductase

[3]

0.4

[4]

0.02048

[5]

C, M

[163] array · 6 items

[0]

Q9D2G2

[1]

Dlst

[2]

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial

[3]

0.4

[4]

0.00639

[5]

M, N, PM

[164] array · 6 items

[0]

Q3UD06

[1]

Atp5c1

[2]

ATP synthase subunit gamma

[3]

0.4

[4]

0.00728

[5]

[165] array · 6 items

[0]

P68372

[1]

Tubb4b

[2]

Tubulin beta-4B chain

[3]

0.4

[4]

0.00008

[5]

[166] array · 6 items

[0]

P99024

[1]

Tubb5

[2]

Tubulin beta-5 chain

[3]

0.4

[4]

0.00005

[5]

CK, C, M

[167] array · 6 items

[0]

P56480

[1]

Atp5b

[2]

ATP synthase subunit beta, mitochondrial

[3]

0.4

[4]

0.00166

[5]

M, PM

[168] array · 6 items

[0]

E9QKR0

[1]

Gnb2

[2]

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2

[3]

0.4

[4]

0.0162

[5]

[169] array · 6 items

[0]

B2RSN3

[1]

Tubb2b

[2]

Tubulin beta chain

[3]

0.4

[4]

0.00013

[5]

[170] array · 6 items

[0]

Q7TMM9

[1]

Tubb2a

[2]

Tubulin beta-2A chain

[3]

0.4

[4]

0.0001

[5]

[171] array · 6 items

[0]

P63017

[1]

Hspa8

[2]

Heat shock cognate 71 kDa protein

[3]

0.4

[4]

0.0001

[5]

CK, C, En, ERS, Ly, N, PM

[172] array · 6 items

[0]

Q3TIC8

[1]

Uqcrc1

[2]

Putative uncharacterized protein

[3]

0.4

[4]

0.00014

[5]

C, M

[173] array · 6 items

[0]

P26443

[1]

Glud1

[2]

Glutamate dehydrogenase 1, mitochondrial

[3]

0.4

[4]

0.00008

[5]

[174] array · 6 items

[0]

Q3TYV5

[1]

Cnp

[2]

2′,3′-cyclic-nucleotide 3′-phosphodiesterase

[3]

0.5

[4]

0.00001

[5]

ERS

[175] array · 6 items

[0]

B7U582

[1]

[2]

Heat shock protein 70-2

[3]

0.5

[4]

0.00001

[5]

[176] array · 6 items

[0]

Q8BH95

[1]

Echs1

[2]

Enoyl-CoA hydratase, mitochondrial

[3]

0.5

[4]

0.03689

[5]

[177] array · 6 items

[0]

Q6P1J1

[1]

Crmp1

[2]

Crmp1 protein

[3]

0.5

[4]

0.00045

[5]

CK, C, N

[178] array · 6 items

[0]

B2CY77

[1]

Rpsa

[2]

Laminin receptor (Fragment)

[3]

0.5

[4]

0.01872

[5]

C, ERS, N, PM

[179] array · 6 items

[0]

Q922F4

[1]

Tubb6

[2]

Tubulin beta-6 chain

[3]

0.5

[4]

0.00002

[5]

[180] array · 6 items

[0]

Q9ERD7

[1]

Tubb3

[2]

Tubulin beta-3 chain

[3]

0.5

[4]

0.00003

[5]

[181] array · 6 items

[0]

Q60930

[1]

Vdac2

[2]

Voltage-dependent anion-selective channel protein 2

[3]

0.5

[4]

0.00247

[5]

[182] array · 6 items

[0]

P14152

[1]

Mdh1

[2]

Malate dehydrogenase, cytoplasmic

[3]

0.5

[4]

0.00092

[5]

C, M

[183] array · 6 items

[0]

A6ZI44

[1]

Aldoa

[2]

Fructose-bisphosphate aldolase

[3]

0.5

[4]

0.00156

[5]

CK, C, ERS, M, N, PM

[184] array · 6 items

[0]

Q80X68

[1]

Csl

[2]

Citrate synthase

[3]

0.5

[4]

0.00001

[5]

[185] array · 6 items

[0]

A2AQ07

[1]

Tubb1

[2]

Tubulin beta-1 chain

[3]

0.5

[4]

0.00009

[5]

[186] array · 6 items

[0]

P01831

[1]

Thy1

[2]

Thy-1 membrane glycoprotein

[3]

0.6

[4]

0.00272

[5]

C, ER, PM

[187] array · 5 items

[0]

A0A1S6GWG6

[1]

Uncharacterized protein

[2]

0,6

[3]

0.00144

[4]

[188] array · 6 items

[0]

Q3UBZ3

[1]

Capza2

[2]

Putative uncharacterized protein

[3]

0.6

[4]

0.03767

[5]

[189] array · 6 items

[0]

Q9D6M3

[1]

Slc25a22

[2]

Mitochondrial glutamate carrier 1

[3]

0.6

[4]

0.02851

[5]

[190] array · 6 items

[0]

O08749

[1]

Dld

[2]

Dihydrolipoyl dehydrogenase, mitochondrial

[3]

0.6

[4]

0.00293

[5]

M, N

[191] array · 6 items

[0]

Q91VA7

[1]

Idh3b

[2]

Isocitrate dehydrogenase [NAD] subunit, mitochondrial

[3]

0.6

[4]

0.0105

[5]

[192] array · 6 items

[0]

O88712

[1]

Ctbp1

[2]

C-terminal-binding protein 1

[3]

0.6

[4]

0.00177

[5]

[193] array · 6 items

[0]

Q8C3L6

[1]

Atp6v1b1

[2]

Putative uncharacterized protein

[3]

0.6

[4]

0.04137

[5]

[194] array · 6 items

[0]

P70333

[1]

Hnrnph2

[2]

Heterogeneous nuclear ribonucleoprotein H2

[3]

0.6

[4]

0.00158

[5]

[195] array · 6 items

[0]

P14094

[1]

Atp1b1

[2]

Sodium/potassium-transporting ATPase subunit beta-1

[3]

0.7

[4]

0.00001

[5]

[196] array · 6 items

[0]

O55100

[1]

Syngr1

[2]

Synaptogyrin-1

[3]

0.7

[4]

0.03643

[5]

[197] array · 6 items

[0]

Q9R0P9

[1]

Uchl1

[2]

Ubiquitin carboxyl-terminal hydrolase isozyme L1

[3]

0.7

[4]

0.00142

[5]

C, ER, PM

[198] array · 6 items

[0]

P05063

[1]

Aldoc

[2]

Fructose-bisphosphate aldolase C

[3]

0.7

[4]

0.00002

[5]

C, M

[199] array · 6 items

[0]

Q61990

[1]

Pcbp2

[2]

Poly(rC)-binding protein 2

[3]

0.8

[4]

0.03331

[5]

C, N

[200] array · 6 items

[0]

Q8R464

[1]

Cadm4

[2]

Cell adhesion molecule 4

[3]

0.8

[4]

0.01837

[5]

[201] array · 6 items

[0]

P21279

[1]

Gnaq

[2]

Guanine nucleotide-binding protein G(q) subunit alpha

[3]

0.9

[4]

0.04159

[5]

C, N, PM

[202] array · 6 items

[0]

Q00898

[1]

Serpina1

[2]

Alpha-1-antitrypsin 1-5

[3]

1.2

[4]

0.04259

[5]

ER, ERS, GA

[203] array · 6 items

[0]

P63330

[1]

Ppp2ca

[2]

Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

[3]

1.4

[4]

0.00163

[5]

CK, C, N, PM

[204] array · 6 items

[0]

P03995

[1]

Gfap

[2]

Glial fibrillary acidic protein

[3]

1.4

[4]

0.00001

[5]

CK, Ly

row_count

205

column_count

numeric_cells

653

header_rows

locator

section[12]/table-wrap[1]#biomolecules-10-00355-t001

[2] object · 16 fields

asset:table:pmid:32111039:2

role

table

format

jats-table

media_type

application/vnd.jats.table+json

uri

null

sha256

sha256:de43767742063922c0004fc46ba280c76acad04aa94ab39fc90ca44db5f8f3f5

bytes

4956

access

open

state

verified

reader

read_table

reader_status

available

identifier

section[13]/table-wrap[1]#biomolecules-10-00355-t002

version

null

note

REACTOME pathway classification of murine NAGLU−/− brain tissue proteome.

structure object · 5 fields

pmcid

PMC7175334

section_index

section_title

3.3. Bioinformatic Analysis of Differentially Abundant Proteins

row_count

column_count

table object · 8 fields

label

Table 2

caption

REACTOME pathway classification of murine NAGLU−/− brain tissue proteome.

rows array · 56 items

[0] array · 4 items

[0]

REACTOME Pathways

[1]

Mus musculus REFLIST

[2]

Client Input

[3]

Client Input (Raw p-Value)

[1] array · 4 items

[0]

Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane (R-MMU-190840)

[1]

[2]

[3]

1.45 × 10−11

[2] array · 4 items

[0]

Citric acid cycle (TCA cycle) (R-MMU-71403)

[1]

[2]

[3]

3.68 × 10−12

[3] array · 4 items

[0]

RHO GTPases activate IQGAPs (R-MMU-5626467)

[1]

[2]

[3]

8.61 × 10−12

[4] array · 4 items

[0]

Carboxyterminal post-translational modifications of tubulin (R-MMU-8955332)

[1]

[2]

[3]

4.00 × 10−10

[5] array · 4 items

[0]

Recycling pathway of L1 (R-MMU-437239)

[1]

[2]

[3]

1.74 × 10−12

[6] array · 4 items

[0]

Lysine catabolism (R-MMU-71064)

[1]

[2]

[3]

7.16 × 10−05

[7] array · 4 items

[0]

HSP90 chaperone cycle for steroid hormone receptors (SHR) (R-MMU-3371497)

[1]

[2]

[3]

1.00 × 10−15

[8] array · 4 items

[0]

COPI-independent Golgi-to-ER retrograde traffic (R-MMU-6811436)

[1]

[2]

[3]

6.42 × 10−13

[9] array · 4 items

[0]

Gluconeogenesis (R-MMU-70263)

[1]

[2]

[3]

3.07 × 10−09

[10] array · 4 items

[0]

Serotonin Neurotransmitter Release Cycle (R-MMU-181429)

[1]

[2]

[3]

1.76 × 10−04

[11] array · 4 items

[0]

Pyruvate metabolism and Citric Acid (TCA) cycle (R-MMU-71406)

[1]

[2]

[3]

4.21 × 10−11

[12] array · 4 items

[0]

GABA synthesis, release, reuptake and degradation (R-MMU-888590)

[1]

[2]

[3]

2.35 × 10−04

[13] array · 4 items

[0]

Dopamine Neurotransmitter Release Cycle (R-MMU-212676)

[1]

[2]

[3]

3.47 × 10−04

[14] array · 4 items

[0]

Glyoxylate metabolism and glycine degradation (R-MMU-389661)

[1]

[2]

[3]

3.64 × 10−05

[15] array · 4 items

[0]

Kinesins (R-MMU-983189)

[1]

[2]

[3]

4.54 × 10−08

[16] array · 4 items

[0]

Intraflagellar transport (R-MMU-5620924)

[1]

[2]

[3]

4.54 × 10−08

[17] array · 4 items

[0]

Recruitment of NuMA to mitotic centrosomes (R-MMU-380320)

[1]

[2]

[3]

6.28 × 10−12

[18] array · 4 items

[0]

RAF activation (R-MMU-5673000)

[1]

[2]

[3]

4.89 × 10−04

[19] array · 4 items

[0]

COPI-mediated anterograde transport (R-MMU-6807878)

[1]

[2]

[3]

2.29 × 10−11

[20] array · 4 items

[0]

The role of GTSE1 in G2/M progression after G2 checkpoint (R-MMU-8852276)

[1]

[2]

[3]

1.45 × 10−08

[21] array · 4 items

[0]

Loss of Nlp from mitotic centrosomes (R-MMU-380259)

[1]

[2]

[3]

1.77 × 10−07

[22] array · 4 items

[0]

AURKA Activation by TPX2 (R-MMU-8854518)

[1]

[2]

[3]

2.33 × 10−07

[23] array · 4 items

[0]

MHC class II antigen presentation (R-MMU-2132295)

[1]

120

[2]

[3]

9.50 × 10−12

[24] array · 4 items

[0]

Recruitment of mitotic centrosome proteins and complexes (R-MMU-380270)

[1]

[2]

[3]

3.91 × 10−07

[25] array · 4 items

[0]

Regulation of PLK1 Activity at G2/M Transition (R-MMU-2565942)

[1]

[2]

[3]

7.92 × 10−07

[26] array · 4 items

[0]

Hedgehog “on” state (R-MMU-5632684)

[1]

103

[2]

[3]

1.91 × 10−07

[27] array · 4 items

[0]

ER to Golgi Anterograde Transport (R-MMU-199977)

[1]

155

[2]

[3]

1.52 × 10−10

[28] array · 4 items

[0]

COPI-dependent Golgi-to-ER retrograde traffic (R-MMU-6811434)

[1]

[2]

[3]

1.30 × 10−06

[29] array · 4 items

[0]

Anchoring of the basal body to the plasma membrane (R-MMU-5620912)

[1]

[2]

[3]

1.40 × 10−06

[30] array · 4 items

[0]

RHO GTPases Activate Formins (R-MMU-5663220)

[1]

133

[2]

[3]

7.13 × 10−09

[31] array · 4 items

[0]

Resolution of Sister Chromatid Cohesion (R-MMU-2500257)

[1]

121

[2]

[3]

4.53 × 10−08

[32] array · 4 items

[0]

Hedgehog “off” state (R-MMU-5610787)

[1]

109

[2]

[3]

2.87 × 10−07

[33] array · 4 items

[0]

Glycolysis (R-MMU-70171)

[1]

[2]

[3]

5.22 × 10−04

[34] array · 4 items

[0]

Separation of Sister Chromatids (R-MMU-2467813)

[1]

185

[2]

[3]

1.36 × 10−07

[35] array · 4 items

[0]

Mitotic Anaphase (R-MMU-68882)

[1]

188

[2]

[3]

1.57 × 10−07

[36] array · 4 items

[0]

Neutrophil degranulation (R-MMU-6798695)

[1]

553

[2]

[3]

3.17 × 10−06

[37] array · 4 items

[0]

Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane (R-MMU-190840)

[1]

[2]

[3]

1.45 × 10−11

[38] array · 4 items

[0]

Citric acid cycle (TCA cycle) (R-MMU-71403)

[1]

[2]

[3]

3.68 × 10−12

[39] array · 4 items

[0]

RHO GTPases activate IQGAPs (R-MMU-5626467)

[1]

[2]

[3]

8.61 × 10−12

[40] array · 4 items

[0]

Carboxyterminal post-translational modifications of tubulin (R-MMU-8955332)

[1]

[2]

[3]

4.00 × 10−10

[41] array · 4 items

[0]

Recycling pathway of L1 (R-MMU-437239)

[1]

[2]

[3]

1.74 × 10−12

[42] array · 4 items

[0]

Lysine catabolism (R-MMU-71064)

[1]

[2]

[3]

7.16 × 10−05

[43] array · 4 items

[0]

Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion (R-MMU-434316)

[1]

[2]

[3]

1.33 × 10−03

[44] array · 4 items

[0]

HSP90 chaperone cycle for steroid hormone receptors (SHR) (R-MMU-3371497)

[1]

[2]

[3]

1.00 × 10−15

[45] array · 4 items

[0]

COPI-independent Golgi-to-ER retrograde traffic (R-MMU-6811436)

[1]

[2]

[3]

6.42 × 10−13

[46] array · 4 items

[0]

Gluconeogenesis (R-MMU-70263)

[1]

[2]

[3]

3.07 × 10−09

[47] array · 4 items

[0]

Serotonin Neurotransmitter Release Cycle (R-MMU-181429)

[1]

[2]

[3]

1.76 × 10−04

[48] array · 4 items

[0]

Pyruvate metabolism and Citric Acid (TCA) cycle (R-MMU-71406)

[1]

[2]

[3]

4.21 × 10−11

[49] array · 4 items

[0]

GABA synthesis, release, reuptake and degradation (R-MMU-888590)

[1]

[2]

[3]

2.35 × 10−04

[50] array · 4 items

[0]

Dopamine Neurotransmitter Release Cycle (R-MMU-212676)

[1]

[2]

[3]

3.47 × 10−04

[51] array · 4 items

[0]

Glyoxylate metabolism and glycine degradation (R-MMU-389661)

[1]

[2]

[3]

3.64 × 10−05

[52] array · 4 items

[0]

Kinesins (R-MMU-983189)

[1]

[2]

[3]

4.54 × 10−08

[53] array · 4 items

[0]

Intraflagellar transport (R-MMU-5620924)

[1]

[2]

[3]

4.54 × 10−08

[54] array · 4 items

[0]

Recruitment of NuMA to mitotic centrosomes (R-MMU-380320)

[1]

[2]

[3]

6.28 × 10−12

[55] array · 4 items

[0]

RAF activation (R-MMU-5673000)

[1]

[2]

[3]

4.89 × 10−04

row_count

column_count

numeric_cells

220

header_rows

locator

section[13]/table-wrap[1]#biomolecules-10-00355-t002

gaps array · 0 items

analysis object · 4 fields

state

partial

methods array · 4 items

[0] object · 10 fields

method-1

family

principal_component_analysis

specific

pca

label

Principal component analysis

dsl_operations array · 1 item

[0]

pca_fit

missing_operations array · 0 items

expressible

true

parameters object · 0 fields

data_shapes array · 1 item

[0]

wide_numeric_matrix

evidence object · 3 fields

score

0.8

band

high

quote

PCA

[1] object · 10 fields

method-2

family

regression_modelling

specific

ols

label

Regression modelling

dsl_operations array · 1 item

[0]

ols_fit

missing_operations array · 0 items

expressible

true

parameters object · 0 fields

data_shapes array · 1 item

[0]

predictors_and_outcome

evidence object · 3 fields

score

0.8

band

high

quote

linear regression

[2] object · 10 fields

method-3

family

network_analysis

specific

ppi_network

label

Network / pathway analysis

dsl_operations array · 3 items

[0]

build_graph

[1]

centrality_scores

[2]

pathway_enrich

missing_operations array · 0 items

expressible

true

parameters object · 0 fields

data_shapes array · 1 item

[0]

edge_list

evidence object · 3 fields

score

0.8

band

high

quote

PPI

[3] object · 10 fields

method-4

family

null

specific

null

label

Two-tailed Student’s t test

dsl_operations array · 0 items

missing_operations array · 0 items

expressible

null

parameters object · 0 fields

data_shapes array · 0 items

evidence object · 3 fields

score

band

verbatim

quote

A Student’s t test was used to select proteins showing significant changes between the analyzed datasets, resulting in two-tailed p values.

targets array · 0 items

gaps array · 1 item

[0]

method.reader_named_unmapped

capability object · 3 fields

state

complete

requirements array · 1 item

[0] object · 6 fields

capability_id

capability:computational_analysis

label

Computational analysis platform

assay_families array · 9 items

[0]

meta_analysis

[1]

machine_learning

[2]

survival_analysis

[3]

statistical_regression

[4]

pca

[5]

molecular_docking

[6]

network_analysis

[7]

differential_expression

[8]

gwas

availability_state

owned

tier_unlocked

candidate

Automated Assays Laravel application and simulated adapters

gaps array · 0 items

readiness object · 8 fields

state

blocked

tier

blocking_axis

data

blocked_on

data:accession_absent

axes object · 3 fields

method object · 5 fields

tier

expressible

true

required_operations array · 1 item

[0]

pca_fit

missing_operations array · 0 items

basis

The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca.

capability object · 4 fields

tier

capability_id

capability:computational_analysis

availability_state

owned

basis

The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.

data object · 6 fields

tier

reachable

false

accessions array · 0 items

resolved_accessions array · 0 items

statements array · 1 item

[0]

Data are available via ProteomeXchange with the identifier PXD017363.

basis

The paper names no accession to its source data, so the data has to come from the authors.

can_run object · 3 fields

dsl_operations array · 1 item

[0]

pca_fit

assets array · 3 items

[0]

source:pmid:32111039

[1]

asset:table:pmid:32111039:1

[2]

asset:table:pmid:32111039:2

steps array · 1 item

[0]

run_analysis

must_build object · 5 fields

dsl_operations array · 0 items

converters array · 0 items

readers array · 0 items

capabilities array · 0 items

data_gaps array · 1 item

[0]

data:geo:None

gaps array · 1 item

[0]

data:accession_absent

review object · 5 fields

state

partial

machine_critique object · 5 fields

kind

extraction_review

reader object · 5 fields

model

MiniMax-M3.1-Flash

provider

minimax

provider_family

minimax

read_at

2026-10-31T18:57:45Z

independence

single_reader

evidence_check object · 2 fields

method

verbatim

availability

verbatim

calls

usage object · 3 fields

prompt_tokens

56140

completion_tokens

1008

cached_tokens

784

human_critique

null

stages array · 1 item

[0] object · 4 fields

extraction

state

complete

reader

MiniMax-M3.1-Flash

provider

minimax

gaps array · 3 items

[0]

review.independent_reader

[1]

review.machine_critique

[2]

review.human_critique

execution object · 5 fields

state

absent

status

not_run

mode

null

runs array · 0 items

gaps array · 1 item

[0]

execution.not_run

provenance object · 7 fields

entities array · 3 items

[0] object · 3 fields

pmid:32111039

type

paper

label

pmid:32111039

[1] object · 3 fields

source:pmid:32111039

type

manuscript

label

PMID 32111039 full text

[2] object · 3 fields

data:geo:None

type

dataset

label

GEO None

activities array · 3 items

[0] object · 4 fields

activity-reading-sci-2026-11-01

type

classification

used array · 3 items

[0] object · 3 fields

pmid:32111039

type

paper

label

pmid:32111039

[1] object · 3 fields

source:pmid:32111039

type

manuscript

label

PMID 32111039 full text

[2] object · 3 fields

data:geo:None

type

dataset

label

GEO None

agent

agent:corpus-assay-engine

[1] object · 4 fields

activity-read-32111039

type

extraction

used array · 1 item

[0]

source:pmid:32111039

agent

agent:minimax-reader

[2] object · 4 fields

activity-resolve-None

type

accession_resolution

used array · 1 item

[0]

data:geo:None

agent

agent:corpus-assay-engine

agents array · 2 items

[0] object · 3 fields

agent:corpus-assay-engine

type

software

label

Corpus assay engine

[1] object · 3 fields

agent:minimax-reader

type

software

label

MiniMax literature reader

source_run_id

reading-sci-2026-11-01

dsl_catalogue_fingerprint

343fb30756ba6ec3

capability_table_fingerprint

2cb3e42f047d2ecf

snapshot_id

ba34b49490d9bfaf

lineage object · 4 fields

parent_id

pmid:32111039

parent_hash

sha256:472d7be1242cc725b01e6b201dc508576b943fc1bb6538213dba810f26e7b42d

fork_of

null

generation

gaps array · 6 items

[0]

execution.not_run

[1]

method.reader_named_unmapped

[2]

review.human_critique

[3]

review.independent_reader

[4]

review.machine_critique

[5]

step:obtain_source_data blocked on data:accession_absent

assays array · 3 items

[0] object · 11 fields

role

data_generation

definition_id

animal_model

definition_version

99e1195c7d6f

definition_digest

null

required_operations array · 0 items

support_state

partial

source_hashes object · 1 field

assay_lexicon

99e1195c7d6f

confidence

0.99

evidence array · 4 items

[0]

eomic Analysis of Mucopolysaccharidosis IIIB Mouse Brain.

[1]

resented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple

[2]

metabolism. The proteome profile of NAGLU-/- mouse brain could pave the way for further studies

[3]

the C57/BL6 background [30]. NAGLU−/− and WT mice were genotyped by PCR [31]. Mice were housed with

order_basis

paper_text_order:4

assay:1

[1] object · 11 fields

role

data_generation

definition_id

western_blot

definition_version

99e1195c7d6f

definition_digest

null

required_operations array · 0 items

support_state

partial

source_hashes object · 1 field

assay_lexicon

99e1195c7d6f

confidence

0.99

evidence array · 2 items

[0]

P03995) differential abundance was proved by Western blotting analysis using an independent set of brain s

[1]

een NAGLU−/− and WT. Supplemental Figure S4: Western blotting of GFAP protein levels in NAGLU−/− and WT br

order_basis

paper_text_order:7707

assay:2

[2] object · 11 fields

role

analysis

definition_id

principal_component_analysis

definition_version

f2132e96ae6c7a4e

definition_digest

null

required_operations array · 1 item

[0]

pca_fit

support_state

supported

source_hashes object · 1 field

dsl_catalogue

f2132e96ae6c7a4e

confidence

0.8

evidence array · 1 item

[0]

PCA

order_basis

consumes_earlier_output

assay:3

Complete file

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32111039", "kind": "science-record", "revision": 7, "content_hash": "sha256:dbc510da81c6e10a7fe806aa4dcc343fc1cdc9d0701f3f39982a861b69ca7d32", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:01:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic Analysis of Mucopolysaccharidosis IIIB Mouse Brain.", "doi": "10.3390/biom10030355", "pmid": "32111039", "authors": ["Valeria De Pasquale", "Michele Costanzo", "Rosa Anna Siciliano", "Maria Fiorella Mazzeo", "Valeria Pistorio", "Laura Bianchi", "Emanuela Marchese", "Margherita Ruoppolo", "Luigi Michele Pavone", "Marianna Caterino"], "journal": "Biomolecules", "year": 2020, "abstract": "Mucopolysaccharidosis IIIB (MPS IIIB) is an inherited metabolic disease due to deficiency of α-N-Acetylglucosaminidase (NAGLU) enzyme with subsequent storage of undegraded heparan sulfate (HS). The main clinical manifestations of the disease are profound intellectual disability and neurodegeneration. A label-free quantitative proteomic approach was applied to compare the proteome profile of brains from MPS IIIB and control mice to identify altered neuropathological pathways of MPS IIIB. Proteins were identified through a bottom up analysis and 130 were significantly under-represented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple bioinformatic analyses allowed to identify three major clusters of the differentially abundant proteins: proteins involved in cytoskeletal regulation, synaptic vesicle trafficking, and energy metabolism. The proteome profile of NAGLU-/- mouse brain could pave the way for further studies aimed at identifying novel therapeutic targets for the MPS IIIB. Data are available via ProteomeXchange with the identifier PXD017363.", "claims": [{"id": "claim-method", "statement": "A Student’s t test was used to select proteins showing significant changes between the analyzed datasets, resulting in two-tailed p values.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32111039", "locator": "sections[7] \"2.5. Quantitative Label-Free Proteomic Analysis\" paragraph 2", "quote": "A Student’s t test was used to select proteins showing significant changes between the analyzed datasets, resulting in two-tailed p values."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with the identifier PXD017363.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32111039", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with the identifier PXD017363."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32111039"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32111039", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biom10030355", "sha256": "sha256:115419db70cdfbfefba1b434eaddf9cd73da450f260b753669d019a76bc11fd4", "bytes": 67353, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biom10030355", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7175334", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32111039:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6b91a3940dd2979cb8cf356268b25a0869b26262a5fa0a48f64cca1838813e53", "bytes": 16535, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#biomolecules-10-00355-t001", "version": null, "note": "Dysregulated proteins in NAGLU−/− mouse brains compared to WT.", "structure": {"pmcid": "PMC7175334", "section_index": 12, "section_title": "3.2. Quantitative Analysis of Differentially Expressed Proteins in Brain Samples from MPS IIIB and WT Mice", "row_count": 205, "column_count": 6}, "table": {"label": "Table 1", "caption": "Dysregulated proteins in NAGLU−/− mouse brains compared to WT.", "rows": [["Swiss-Prot Code", "Gene Name", "Protein Description", "Fold NSAF", "p Value", "Subcellular Localization"], ["Q545B6", "Stmn1", "Stathmin", "−12.6", "0.00002", "CK"], ["Q9QYX7", "Pclo", "Protein piccolo", "−8.4", "0.00101", "CK, GA"], ["Q6P9K8", "Caskin1", "Caskin-1", "−3.8", "0.00262", "CK"], ["A8DUK2", "Hbbt1", "Beta-globin", "−3.4", "0.00008", "C"], ["Q4VAE3", "Tmem65", "Transmembrane protein 65", "−3.3", "0.00374", "M, PM"], ["Q8CHF1", "mKIAA0531", "Kinesin-like protein (Fragment)", "−3.2", "0.00232", "CK"], ["P17563", "Selenbp1", "Selenium-binding protein 1", "−3.2", "0.00046", "CK, N"], ["Q4KMM3", "Oxr1", "Oxidation resistance protein 1", "−3", "0.00036", "M, N"], ["A2AS98", "Nckap1", "Nck-associated protein 1", "−2.9", "0.00209", "CK, PM"], ["C7G3P1", "Ppfia3", "MKIAA0654 protein (Fragment)", "−2.6", "0.00328", "CK"], ["Q8BVQ5", "Ppme1", "Protein phosphatase methylesterase 1", "−2.5", "0.00345", "N"], ["Q3UVN5", "Nsfl1c", "Putative uncharacterized protein", "−2.5", "0.00002", "CK, GA, N"], ["Q9R0Q6", "Arpc1a", "Actin-related protein 2/3 complex subunit 1A", "−2.4", "0.00036", "CK, N, PM"], ["Q3TF14", "Ahcy", "Adenosylhomocysteinase", "−2.4", "0.00329", "CK, N"], ["Q9CX86", "Hnrnpa0", "Heterogeneous nuclear ribonucleoprotein A0", "−2.4", "0.00165", "N"], ["Q9Z1B3", "Plcb1", "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1", "−2.4", "0.00671", "CK, N, PM"], ["O54991", "Cntnap1", "Contactin-associated protein 1", "−2.3", "0.00626", "PM"], ["B0V2P5", "Dmxl2", "DmX-like protein 2", "−2.3", "0.01109", "PM"], ["E9Q8N8", "Slc4a4", "Anion exchange protein", "−2.3", "0.0011", "PM"], ["B1AQX9", "Srcin1", "SRC kinase-signaling inhibitor 1", "−2.3", "0.0004", "CK"], ["P24472", "Gsta4", "Glutathione S-transferase A4", "−2.3", "0.00125", "M"], ["Q3UK83", "Hnrnpa1", "Putative uncharacterized protein", "−2.2", "0.00047", "ERS, N"], ["D3Z4J3", "Myo5a", "Unconventional myosin-Va", "−2.2", "0.00636", "CK, C, ER, En, GA, Ly, Pe"], ["Q61411", "Hras", "GTPase HRas", "−2.2", "0.00583", "C, GA, N, PM"], ["Q9Z0X1", "Aifm1", "Apoptosis-inducing factor 1, mitochondrial", "−2.1", "0.00398", "CK, M, N"], ["B2L107", "Vsnl1", "Visinin-like protein 1", "−2.1", "0.00018", "C"], ["Q9DBF1", "Aldh7a", "Alpha-aminoadipic semialdehyde dehydrogenase", "−2.1", "0.02264", "C, M, N"], ["Q3TJF2", "Ola1", "Obg-like ATPase 1", "−2.1", "0.00001", "CK, C, N"], ["Q8VDD5", "Myh9", "Myosin-9", "−2", "0.01358", "C, CK, N, PM"], ["Q9JJK2", "Lancl2", "LanC-like protein 2", "−2", "0.00232", "C, CK, N, PM"], ["E9Q2L2", "Dlg2", "Disks large homolog 2", "−2", "0.00218", "PM"], ["Q91VR5", "Ddx1", "ATP-dependent RNA helicase DDX1", "−2", "0.00216", "C, M, N"], ["Q9JHU4", "Dync1h1", "Cytoplasmic dynein 1 heavy chain 1", "−2", "0.00407", "CK, N"], ["Q99PU5", "Acsbg1", "Long-chain-fatty-acid--CoA ligase ACSBG1", "−1.9", "0.01942", "ER, PM"], ["Q64010", "Crk", "Adapter molecule crk", "−1.9", "0.0031", "CK, PM"], ["P14733", "Lmnb1", "Lamin-B1", "−1.9", "0.02293", "CK, N"], ["P54775", "Psmc4", "26S protease regulatory subunit 6B", "−1.9", "0.03099", "CK, N"], ["A0A1S6GWI0", "Ndufa8", "NADH dehydrogenase (Ubiquinone) 1 alpha subcomplex, 8", "−1.8", "0.00156", "M"], ["Q3U741", "Ddx17", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17, isoform CRA_a", "−1.8", "0.00085", "C, N"], ["Q3TIQ2", "Rpl12", "Putative uncharacterized protein", "−1.8", "0.01139", "C, N"], ["P70168", "Kpnb1", "Importin subunit beta-1", "−1.7", "0.00011", "C, M, N"], ["Q80TZ3", "Dnajc6", "Putative tyrosine-protein phosphatase auxilin", "−1.7", "0.00164", "C"], ["Q5DTG0", "Atp8a1", "Phospholipid-transporting ATPase (Fragment)", "−1.7", "0.00428", "ER, GA, PM"], ["Q9QXS1", "Plec", "Plectin", "−1.7", "0.00377", "C, CK, PM"], ["Q921F2", "Tardbp", "TAR DNA-binding protein 43", "−1.7", "0.00786", "N"], ["B2RX08", "Sptb", "Spectrin beta chain", "−1.7", "0.00319", "C, CK, PM"], ["Q3TKG4", "Psmc3", "Putative uncharacterized protein (Fragment)", "−1.6", "0.00396", "N"], ["Q3UH59", "Myh10", "Myosin-10", "−1.6", "0.02527", "C, CK, PM"], ["Q9JM76", "Arpc3", "Actin-related protein 2/3 complex subunit 3", "−1.6", "0.01437", "C, N"], ["A0A1S6GWJ8", "Uncharacterized protein", "–1,5", "0.02713", ""], ["Q3UN60", "Mpp6", "Membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6), isoform CRA_b", "−1.5", "0.00085", "PM"], ["Q91XV3", "Basp1", "Brain acid soluble protein 1", "−1.5", "0.00001", "N, PM"], ["Q07076", "Anxa7", "Annexin A7", "−1.5", "0.01183", "C, ER, ERS, N, PM"], ["Q3UY05", "Ndufs8", "Putative uncharacterized protein", "−1.4", "0.00008", "M"], ["A0A0R4J0Q5", "Lmnb2", "Lamin-B2", "−1.4", "0.03275", "CK, N"], ["Q4FJX9", "Sod2", "Superoxide dismutase", "−1.4", "0.01379", "M"], ["Q91VN4", "Chchd6", "MICOS complex subunit Mic25", "−1.4", "0.01573", "C, M"], ["O88737", "Bsn", "Protein bassoon", "−1.3", "0.00915", "C, GA"], ["Q3UWW9", "Psmd11", "Putative uncharacterized protein", "−1.3", "0.01386", "C, N"], ["O08788", "Dctn1", "Dynactin subunit 1", "−1.3", "0.01243", "CK, C, ERS, N"], ["A0A0R4J275", "Ndufa12", "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12", "−1.3", "0.0197", "C, M"], ["Q63932", "Map2k2", "Dual specificity mitogen-activated protein kinase kinase 2", "−1.3", "0.01951", "CK, C, ER, En, GA, M, N, PM"], ["Q61361", "Bcan", "Brevican core protein", "−1.3", "0.01264", "ERS"], ["Q3V117", "Acly", "ATP-citrate synthase", "−1.3", "0.0078", "C, M, N, PM"], ["Q8R570", "Snap47", "Synaptosomal-associated protein 47", "−1.3", "0.00248", "C, PM"], ["Q9DCS9", "Ndufb10", "NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10", "−1.2", "0.01688", "M"], ["P14824", "Anxa6", "Annexin A6", "−1.2", "0.01378", "C, En, ERS, Ly, M, N, PM"], ["P54071", "Idh2", "Isocitrate dehydrogenase [NADP], mitochondrial", "−1.2", "0.00039", "C, M, Pe"], ["Q7TSJ2", "Map6", "Microtubule-associated protein 6", "−1.2", "0.00159", "CK, GA"], ["Q8BGN3", "Enpp6", "Ectonucleotide pyrophosphatase/phosphodiesterase family member 6", "−1.2", "0.03099", "ERS, PM"], ["Q9CZD3", "Gars", "Glycine--tRNA ligase", "−1.2", "0.01474", "C, ERS, M"], ["A0A0R4J083", "Acadl", "Long-chain-specific acyl-CoA dehydrogenase, mitochondrial", "−1.2", "0.03611", "M"], ["Q8CGK3", "Lonp1", "Lon protease homolog, mitochondrial", "−1.1", "0.01936", "C, M, N"], ["E9Q7Q3", "Tpm3", "Tropomyosin alpha-3 chain", "−1.1", "0.00355", "CK, C"], ["Q8BWT1", "Acaa2", "3-ketoacyl-CoA thiolase, mitochondrial", "−1.1", "0.04478", "M"], ["P61226", "Rap2b", "Ras-related protein Rap-2b", "−1.1", "0.03025", "C, En, ERS, PM"], ["Q8R5C5", "Actr1b", "Beta-centractin", "−1.1", "0.00172", "CK"], ["E9Q0J5", "Kif21a", "Kinesin-like protein KIF21A", "−1.1", "0.04345", "CK, C, PM"], ["B9EKR1", "Ptprz1", "Receptor-type tyrosine-protein phosphatase zeta", "−1.1", "0.01214", "ERS, PM"], ["Q6ZQ38", "Cand1", "Cullin-associated NEDD8-dissociated protein 1", "−1", "0.00177", "C, GA, N"], ["Q9JI91", "Actn2", "Alpha-actinin-2", "−1", "0.00286", "CK, PM"], ["P68040", "Rack1", "Receptor of activated protein C kinase 1", "−1", "0.03823", "CK, M, N, PM"], ["E9PUL5", "Prrt2", "Proline-rich transmembrane protein 2", "−1", "0.0411", "PM"], ["F6SEU4", "Syngap1", "Ras/Rap GTPase-activating protein SynGAP", "−1", "0.03268", "PM"], ["Q8CHG1", "Dclk1", "MKIAA0369 protein (Fragment)", "−1", "0.02306", "PM"], ["Q61490", "Alcam", "CD166 antigen", "−1", "0.03414", "PM"], ["D3Z656", "Synj1", "Synaptojanin-1", "−1", "0.02126", "PM"], ["H3BIV5", "Akap5", "A-kinase anchor protein 5", "−1", "0.01709", "CK, PM"], ["Q8VD37", "Sgip1", "SH3-containing GRB2-like protein 3-interacting protein 1", "−1", "0.04017", "CK, PM"], ["W6PPR4", "Ank3", "480-kDa ankyrinG", "−1", "0.00579", "CK, C, PM"], ["Q9CWS0", "Ddah1", "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1", "−0.9", "0.04649", "M"], ["Q11011", "Npepps", "Puromycin-sensitive aminopeptidase", "−0.9", "0.00505", "C, N"], ["Q3TXE5", "Canx", "Putative uncharacterized protein", "−0.9", "0.00488", "ER, PM"], ["Q3UAG2", "Pgd", "6-phosphogluconate dehydrogenase, decarboxylating", "−0.9", "0.02403", "C"], ["Q99JX6", "Anxa6", "Annexin", "−0.9", "0.04313", "C, En, ERS, Ly, M, N, PM"], ["A0A0G2JEG8", "Amph", "Amphiphysin", "−0.9", "0.00912", "CK, PM"], ["Q99P72", "Rtn4", "Reticulon-4", "−0.9", "0.01061", "ER, N, PM"], ["Q49S98", "Slc32a1", "Putative uncharacterized protein", "−0.9", "0.04098", "PM"], ["B2RQQ5", "Map1b", "Microtubule-associated protein 1B", "−0.9", "0.03443", "CK, C, PM"], ["D3Z2H9", "Tpm3", "Uncharacterized protein", "−0.9", "0.02982", "CK, C"], ["Q6ZQ61", "Matr3", "MCG121979, isoform CRA_c (Fragment)", "−0.8", "0.01811", "N"], ["Q3TE45", "Sdhb", "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial", "−0.8", "0.01667", "M, N, PM"], ["Q0VF55", "Atp2b3", "Calcium-transporting ATPase", "−0.8", "0.03416", "PM"], ["Q3UEG9", "Flot2", "Putative uncharacterized protein", "−0.8", "0.02632", "CK, En, PM"], ["Q91V61", "Sfxn3", "Sideroflexin-3", "−0.8", "0.00937", "M"], ["P61164", "Actr1a", "Alpha-centractin", "−0.8", "0.03531", "CK"], ["Q571M2", "Hspa4", "MKIAA4025 protein (Fragment)", "−0.7", "0.00487", "C, ERS, N"], ["Q9Z2Y3", "Homer1", "Homer protein homolog 1", "−0.7", "0.01584", "C, PM"], ["E9Q455", "Tpm1", "Tropomyosin alpha-1 chain", "−0.7", "0.04225", "C"], ["A2A5Y6", "Mapt", "Microtubule-associated protein", "−0.7", "0.04838", "CK, C, N, PM"], ["A0A1S6GWH1", "Uncharacterized protein", "–0,7", "0.02404", ""], ["P35486", "Pdha1", "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial", "−0.6", "0.00552", "M, N"], ["Q8CC13", "Ap1b1", "AP complex subunit beta", "−0.6", "0.03216", "C, GA"], ["E9Q2W9", "Actn4", "Alpha-actinin-4 (Fragment)", "−0.6", "0.00847", "CK, C, N"], ["Q8BVE3", "Atp6v1h", "V-type proton ATPase subunit H", "−0.6", "0.02175", "C, Ly"], ["A0A0A6YY91", "Ncam1", "Neural cell adhesion molecule 1 (Fragment)", "−0.6", "0.0182", "CK, PM"], ["Q3TYK4", "Prkar1a", "Putative uncharacterized protein", "−0.6", "0.01177", "CK, C, PM"], ["P12960", "Cntn1", "Contactin-1", "−0.6", "0.02931", "PM"], ["Q3TPZ5", "Dctn2", "Dynactin 2", "−0.6", "0.00054", "CK, C"], ["A0A1L1SV25", "Actn4", "Alpha-actinin-4", "−0.6", "0.0286", "CK, C, N"], ["P19246", "Nefh", "Neurofilament heavy polypeptide", "−0.5", "0.04106", "CK, M, N, PM"], ["A0A0R4J117", "Igsf8", "Immunoglobulin superfamily member 8", "−0.5", "0.04908", "PM"], ["Q68FG2", "Sptbn2", "Spectrin beta chain", "−0.5", "0.04372", "CK, C, ER, En, GA"], ["Q80YU5", "Mog", "Myelin oligodendrocyte glycoprotein (Fragment)", "−0.5", "0.02477", "C, ER, M, PM"], ["E9QB01", "Ncam1", "Neural cell adhesion molecule 1", "−0.5", "0.03648", "C, PM"], ["Q01853", "Vcp", "Transitional endoplasmic reticulum ATPase", "−0.5", "0.03249", "C, ER, N"], ["P09041", "Pgk2", "Phosphoglycerate kinase 2", "−0.4", "0.03696", "C"], ["Q7TPR4", "Actn1", "Alpha-actinin-1", "−0.4", "0.01557", "CK, N, PM"], ["P63011", "Rab3a", "Ras-related protein Rab-3A", "−0.4", "0.0162", "C, En, Ly, PM"], ["P09411", "Pgk1", "Phosphoglycerate kinase 1", "−0.3", "0.01617", "C, ERS, PM"], ["O08599", "Stxbp1", "Syntaxin-binding protein 1", "0.1", "0.03134", "CK, C, M, PM"], ["A0A0A0MQA5", "Tuba4a", "Tubulin alpha chain (Fragment)", "0.2", "0.01472", "CK"], ["P68369", "Tuba1a", "Tubulin alpha-1A chain", "0.2", "0.02299", "CK, En"], ["Q52L87", "Tuba1c", "Tubulin alpha chain", "0.3", "0.0146", "CK, N"], ["P50396", "Gdi1", "Rab GDP dissociation inhibitor alpha", "0.3", "0.03464", "GA"], ["P60710", "Actb", "Actin, cytoplasmic 1", "0.3", "0.02793", "CK, C, N, PM"], ["Q9CZU6", "Cs", "Citrate synthase, mitochondrial", "0.3", "0.00075", "M"], ["P05202", "Got2", "Aspartate aminotransferase, mitochondrial", "0.3", "0.03387", "M, PM"], ["P63038", "Hspd1", "60 kDa heat shock protein, mitochondrial", "0.3", "0.02215", "CK, ER, En, ERS, GA, M, PM"], ["E9Q912", "Rap1gds1", "RAP1, GTP-GDP dissociation stimulator 1", "0.3", "0.00467", "CK, ER, M"], ["B2CSK2", "", "Heat shock protein 1-like protein", "0.3", "0.00172", ""], ["O88935", "Syn1", "Synapsin-1", "0.3", "0.03624", "CK, C, GA, N"], ["P68033", "Actc1", "Actin, alpha cardiac muscle 1", "0.3", "0.00986", "CK"], ["P08249", "Mdh2", "Malate dehydrogenase, mitochondrial", "0.3", "0.00731", "M"], ["Q03265", "Atp5a1", "ATP synthase subunit alpha, mitochondrial", "0.3", "0.00169", "M, N, PM"], ["Q99KI0", "Aco2", "Aconitate hydratase, mitochondrial", "0.3", "0.00087", "C, M"], ["P17879", "Hspa1b", "Heat shock 70 kDa protein 1B", "0.4", "0.00362", "CK, C, M, N, PM"], ["O08553", "Dpysl2", "Dihydropyrimidinase-related protein 2", "0.4", "0.00004", "CK, C, M, PM"], ["Q5FW97", "EG433182", "Enolase 1, alpha non-neuron", "0.4", "0.00346", "C"], ["Q64332", "Syn2", "Synapsin-2", "0.4", "0.01708", "PM"], ["Q3TQ70", "Gnb1", "Beta1 subnuit of GTP-binding protein", "0.4", "0.01897", "PM"], ["P62631", "Eef1a2", "Elongation factor 1-alpha 2", "0.4", "0.00011", "N"], ["P80316", "Cct5", "T-complex protein 1 subunit epsilon", "0.4", "0.04942", "CK, C"], ["Q8CE19", "Syn2", "Putative uncharacterized protein", "0.4", "0.02198", "PM"], ["Q3UA81", "Eef1a1", "Elongation factor 1-alpha", "0.4", "0.00003", "CK, C, M, PM"], ["Q8C2Q7", "Hnrnph1", "Heterogeneous nuclear ribonucleoprotein H", "0.4", "0.01261", "C, N"], ["Q9D6F9", "Tubb4a", "Tubulin beta-4A chain", "0.4", "0.00031", "CK"], ["P17751", "Tpi1", "Triosephosphate isomerase", "0.4", "0.00008", "C"], ["P48774", "Gstm5", "Glutathione S-transferase Mu 5", "0.4", "0.01045", "C, ERS"], ["P18872", "Gnao1", "Guanine nucleotide-binding protein G(o) subunit alpha", "0.4", "0.00334", "PM"], ["Q3UYK6", "Slc1a2", "Amino acid transporter", "0.4", "0.03711", "PM"], ["Q8BVI4", "Qdpr", "Dihydropteridine reductase", "0.4", "0.02048", "C, M"], ["Q9D2G2", "Dlst", "Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial", "0.4", "0.00639", "M, N, PM"], ["Q3UD06", "Atp5c1", "ATP synthase subunit gamma", "0.4", "0.00728", "M"], ["P68372", "Tubb4b", "Tubulin beta-4B chain", "0.4", "0.00008", "CK"], ["P99024", "Tubb5", "Tubulin beta-5 chain", "0.4", "0.00005", "CK, C, M"], ["P56480", "Atp5b", "ATP synthase subunit beta, mitochondrial", "0.4", "0.00166", "M, PM"], ["E9QKR0", "Gnb2", "Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2", "0.4", "0.0162", "PM"], ["B2RSN3", "Tubb2b", "Tubulin beta chain", "0.4", "0.00013", "CK"], ["Q7TMM9", "Tubb2a", "Tubulin beta-2A chain", "0.4", "0.0001", "CK"], ["P63017", "Hspa8", "Heat shock cognate 71 kDa protein", "0.4", "0.0001", "CK, C, En, ERS, Ly, N, PM"], ["Q3TIC8", "Uqcrc1", "Putative uncharacterized protein", "0.4", "0.00014", "C, M"], ["P26443", "Glud1", "Glutamate dehydrogenase 1, mitochondrial", "0.4", "0.00008", "M"], ["Q3TYV5", "Cnp", "2′,3′-cyclic-nucleotide 3′-phosphodiesterase", "0.5", "0.00001", "ERS"], ["B7U582", "", "Heat shock protein 70-2", "0.5", "0.00001", ""], ["Q8BH95", "Echs1", "Enoyl-CoA hydratase, mitochondrial", "0.5", "0.03689", "M"], ["Q6P1J1", "Crmp1", "Crmp1 protein", "0.5", "0.00045", "CK, C, N"], ["B2CY77", "Rpsa", "Laminin receptor (Fragment)", "0.5", "0.01872", "C, ERS, N, PM"], ["Q922F4", "Tubb6", "Tubulin beta-6 chain", "0.5", "0.00002", "CK"], ["Q9ERD7", "Tubb3", "Tubulin beta-3 chain", "0.5", "0.00003", "CK"], ["Q60930", "Vdac2", "Voltage-dependent anion-selective channel protein 2", "0.5", "0.00247", "M"], ["P14152", "Mdh1", "Malate dehydrogenase, cytoplasmic", "0.5", "0.00092", "C, M"], ["A6ZI44", "Aldoa", "Fructose-bisphosphate aldolase", "0.5", "0.00156", "CK, C, ERS, M, N, PM"], ["Q80X68", "Csl", "Citrate synthase", "0.5", "0.00001", "N"], ["A2AQ07", "Tubb1", "Tubulin beta-1 chain", "0.5", "0.00009", "CK"], ["P01831", "Thy1", "Thy-1 membrane glycoprotein", "0.6", "0.00272", "C, ER, PM"], ["A0A1S6GWG6", "Uncharacterized protein", "0,6", "0.00144", ""], ["Q3UBZ3", "Capza2", "Putative uncharacterized protein", "0.6", "0.03767", "CK"], ["Q9D6M3", "Slc25a22", "Mitochondrial glutamate carrier 1", "0.6", "0.02851", "M"], ["O08749", "Dld", "Dihydrolipoyl dehydrogenase, mitochondrial", "0.6", "0.00293", "M, N"], ["Q91VA7", "Idh3b", "Isocitrate dehydrogenase [NAD] subunit, mitochondrial", "0.6", "0.0105", "M"], ["O88712", "Ctbp1", "C-terminal-binding protein 1", "0.6", "0.00177", "N"], ["Q8C3L6", "Atp6v1b1", "Putative uncharacterized protein", "0.6", "0.04137", "PM"], ["P70333", "Hnrnph2", "Heterogeneous nuclear ribonucleoprotein H2", "0.6", "0.00158", "N"], ["P14094", "Atp1b1", "Sodium/potassium-transporting ATPase subunit beta-1", "0.7", "0.00001", "PM"], ["O55100", "Syngr1", "Synaptogyrin-1", "0.7", "0.03643", "PM"], ["Q9R0P9", "Uchl1", "Ubiquitin carboxyl-terminal hydrolase isozyme L1", "0.7", "0.00142", "C, ER, PM"], ["P05063", "Aldoc", "Fructose-bisphosphate aldolase C", "0.7", "0.00002", "C, M"], ["Q61990", "Pcbp2", "Poly(rC)-binding protein 2", "0.8", "0.03331", "C, N"], ["Q8R464", "Cadm4", "Cell adhesion molecule 4", "0.8", "0.01837", "PM"], ["P21279", "Gnaq", "Guanine nucleotide-binding protein G(q) subunit alpha", "0.9", "0.04159", "C, N, PM"], ["Q00898", "Serpina1", "Alpha-1-antitrypsin 1-5", "1.2", "0.04259", "ER, ERS, GA"], ["P63330", "Ppp2ca", "Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform", "1.4", "0.00163", "CK, C, N, PM"], ["P03995", "Gfap", "Glial fibrillary acidic protein", "1.4", "0.00001", "CK, Ly"]], "row_count": 205, "column_count": 6, "numeric_cells": 653, "header_rows": 1, "locator": "section[12]/table-wrap[1]#biomolecules-10-00355-t001"}}, {"id": "asset:table:pmid:32111039:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:de43767742063922c0004fc46ba280c76acad04aa94ab39fc90ca44db5f8f3f5", "bytes": 4956, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#biomolecules-10-00355-t002", "version": null, "note": "REACTOME pathway classification of murine NAGLU−/− brain tissue proteome.", "structure": {"pmcid": "PMC7175334", "section_index": 13, "section_title": "3.3. Bioinformatic Analysis of Differentially Abundant Proteins", "row_count": 56, "column_count": 4}, "table": {"label": "Table 2", "caption": "REACTOME pathway classification of murine NAGLU−/− brain tissue proteome.", "rows": [["REACTOME Pathways", "Mus musculus REFLIST", "Client Input", "Client Input (Raw p-Value)"], ["Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane (R-MMU-190840)", "14", "7", "1.45 × 10−11"], ["Citric acid cycle (TCA cycle) (R-MMU-71403)", "22", "8", "3.68 × 10−12"], ["RHO GTPases activate IQGAPs (R-MMU-5626467)", "25", "8", "8.61 × 10−12"], ["Carboxyterminal post-translational modifications of tubulin (R-MMU-8955332)", "25", "7", "4.00 × 10−10"], ["Recycling pathway of L1 (R-MMU-437239)", "34", "9", "1.74 × 10−12"], ["Lysine catabolism (R-MMU-71064)", "12", "3", "7.16 × 10−05"], ["HSP90 chaperone cycle for steroid hormone receptors (SHR) (R-MMU-3371497)", "51", "12", "1.00 × 10−15"], ["COPI-independent Golgi-to-ER retrograde traffic (R-MMU-6811436)", "47", "10", "6.42 × 10−13"], ["Gluconeogenesis (R-MMU-70263)", "35", "7", "3.07 × 10−09"], ["Serotonin Neurotransmitter Release Cycle (R-MMU-181429)", "17", "3", "1.76 × 10−04"], ["Pyruvate metabolism and Citric Acid (TCA) cycle (R-MMU-71406)", "51", "9", "4.21 × 10−11"], ["GABA synthesis, release, reuptake and degradation (R-MMU-888590)", "19", "3", "2.35 × 10−04"], ["Dopamine Neurotransmitter Release Cycle (R-MMU-212676)", "22", "3", "3.47 × 10−04"], ["Glyoxylate metabolism and glycine degradation (R-MMU-389661)", "30", "4", "3.64 × 10−05"], ["Kinesins (R-MMU-983189)", "54", "7", "4.54 × 10−08"], ["Intraflagellar transport (R-MMU-5620924)", "54", "7", "4.54 × 10−08"], ["Recruitment of NuMA to mitotic centrosomes (R-MMU-380320)", "86", "11", "6.28 × 10−12"], ["RAF activation (R-MMU-5673000)", "25", "3", "4.89 × 10−04"], ["COPI-mediated anterograde transport (R-MMU-6807878)", "98", "11", "2.29 × 10−11"], ["The role of GTSE1 in G2/M progression after G2 checkpoint (R-MMU-8852276)", "72", "8", "1.45 × 10−08"], ["Loss of Nlp from mitotic centrosomes (R-MMU-380259)", "67", "7", "1.77 × 10−07"], ["AURKA Activation by TPX2 (R-MMU-8854518)", "70", "7", "2.33 × 10−07"], ["MHC class II antigen presentation (R-MMU-2132295)", "120", "12", "9.50 × 10−12"], ["Recruitment of mitotic centrosome proteins and complexes (R-MMU-380270)", "76", "7", "3.91 × 10−07"], ["Regulation of PLK1 Activity at G2/M Transition (R-MMU-2565942)", "85", "7", "7.92 × 10−07"], ["Hedgehog “on” state (R-MMU-5632684)", "103", "8", "1.91 × 10−07"], ["ER to Golgi Anterograde Transport (R-MMU-199977)", "155", "12", "1.52 × 10−10"], ["COPI-dependent Golgi-to-ER retrograde traffic (R-MMU-6811434)", "92", "7", "1.30 × 10−06"], ["Anchoring of the basal body to the plasma membrane (R-MMU-5620912)", "93", "7", "1.40 × 10−06"], ["RHO GTPases Activate Formins (R-MMU-5663220)", "133", "10", "7.13 × 10−09"], ["Resolution of Sister Chromatid Cohesion (R-MMU-2500257)", "121", "9", "4.53 × 10−08"], ["Hedgehog “off” state (R-MMU-5610787)", "109", "8", "2.87 × 10−07"], ["Glycolysis (R-MMU-70171)", "63", "4", "5.22 × 10−04"], ["Separation of Sister Chromatids (R-MMU-2467813)", "185", "10", "1.36 × 10−07"], ["Mitotic Anaphase (R-MMU-68882)", "188", "10", "1.57 × 10−07"], ["Neutrophil degranulation (R-MMU-6798695)", "553", "14", "3.17 × 10−06"], ["Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane (R-MMU-190840)", "14", "7", "1.45 × 10−11"], ["Citric acid cycle (TCA cycle) (R-MMU-71403)", "22", "8", "3.68 × 10−12"], ["RHO GTPases activate IQGAPs (R-MMU-5626467)", "25", "8", "8.61 × 10−12"], ["Carboxyterminal post-translational modifications of tubulin (R-MMU-8955332)", "25", "7", "4.00 × 10−10"], ["Recycling pathway of L1 (R-MMU-437239)", "34", "9", "1.74 × 10−12"], ["Lysine catabolism (R-MMU-71064)", "12", "3", "7.16 × 10−05"], ["Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion (R-MMU-434316)", "8", "2", "1.33 × 10−03"], ["HSP90 chaperone cycle for steroid hormone receptors (SHR) (R-MMU-3371497)", "51", "12", "1.00 × 10−15"], ["COPI-independent Golgi-to-ER retrograde traffic (R-MMU-6811436)", "47", "10", "6.42 × 10−13"], ["Gluconeogenesis (R-MMU-70263)", "35", "7", "3.07 × 10−09"], ["Serotonin Neurotransmitter Release Cycle (R-MMU-181429)", "17", "3", "1.76 × 10−04"], ["Pyruvate metabolism and Citric Acid (TCA) cycle (R-MMU-71406)", "51", "9", "4.21 × 10−11"], ["GABA synthesis, release, reuptake and degradation (R-MMU-888590)", "19", "3", "2.35 × 10−04"], ["Dopamine Neurotransmitter Release Cycle (R-MMU-212676)", "22", "3", "3.47 × 10−04"], ["Glyoxylate metabolism and glycine degradation (R-MMU-389661)", "30", "4", "3.64 × 10−05"], ["Kinesins (R-MMU-983189)", "54", "7", "4.54 × 10−08"], ["Intraflagellar transport (R-MMU-5620924)", "54", "7", "4.54 × 10−08"], ["Recruitment of NuMA to mitotic centrosomes (R-MMU-380320)", "86", "11", "6.28 × 10−12"], ["RAF activation (R-MMU-5673000)", "25", "3", "4.89 × 10−04"]], "row_count": 56, "column_count": 4, "numeric_cells": 220, "header_rows": 1, "locator": "section[13]/table-wrap[1]#biomolecules-10-00355-t002"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-2", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "linear regression"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-4", "family": null, "specific": null, "label": "Two-tailed Student’s t test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A Student’s t test was used to select proteins showing significant changes between the analyzed datasets, resulting in two-tailed p values."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["Data are available via ProteomeXchange with the identifier PXD017363."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:32111039", "asset:table:pmid:32111039:1", "asset:table:pmid:32111039:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:57:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 56140, "completion_tokens": 1008, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32111039", "type": "paper", "label": "pmid:32111039"}, {"id": "source:pmid:32111039", "type": "manuscript", "label": "PMID 32111039 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32111039", "type": "paper", "label": "pmid:32111039"}, {"id": "source:pmid:32111039", "type": "manuscript", "label": "PMID 32111039 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32111039", "type": "extraction", "used": ["source:pmid:32111039"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32111039", "parent_hash": "sha256:472d7be1242cc725b01e6b201dc508576b943fc1bb6538213dba810f26e7b42d", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["eomic Analysis of Mucopolysaccharidosis IIIB Mouse Brain.", "resented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple", "metabolism. The proteome profile of NAGLU-/- mouse brain could pave the way for further studies", "the C57/BL6 background [30]. NAGLU−/− and WT mice were genotyped by PCR [31]. Mice were housed with"], "order_basis": "paper_text_order:4", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["P03995) differential abundance was proved by Western blotting analysis using an independent set of brain s", "een NAGLU−/− and WT. Supplemental Figure S4: Western blotting of GFAP protein levels in NAGLU−/− and WT br"], "order_basis": "paper_text_order:7707", "id": "assay:2"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["PCA"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}