Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:25100957

Environmental enrichment alters protein expression as well as the proteomic response to cocaine in rat nucleus accumbens.

Cheryl F Lichti · Xiuzhen Fan · Robert D English · Yafang Zhang · Dingge Li · Fanping Kong · Mala Sinha · Clark R Andersen · Heidi Spratt · Bruce A Luxon · Thomas A Green

Frontiers in behavioral neuroscience · 2014 doi:10.3389/fnbeh.2014.00246

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

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.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
sci_version
1.2
id
pmid:25100957
kind
science-record
revision
8
content_hash
sha256:91eb50c3d2b07e015c07c93eb0c6ef65165411917fe6cab435228cb02d243d18
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:05Z
updated_at
2026-11-01T22:42:05Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Environmental enrichment alters protein expression as well as the proteomic response to cocaine in rat nucleus accumbens.
doi
10.3389/fnbeh.2014.00246
pmid
25100957
authors array · 11 items
[0]
Cheryl F Lichti
[1]
Xiuzhen Fan
[2]
Robert D English
[3]
Yafang Zhang
[4]
Dingge Li
[5]
Fanping Kong
[6]
Mala Sinha
[7]
Clark R Andersen
[8]
Heidi Spratt
[9]
Bruce A Luxon
[10]
Thomas A Green
journal
Frontiers in behavioral neuroscience
year
2014
abstract
Prior research demonstrated that environmental enrichment creates individual differences in behavior leading to a protective addiction phenotype in rats. Understanding the mechanisms underlying this phenotype will guide selection of targets for much-needed novel pharmacotherapeutics. The current study investigates differences in proteome expression in the nucleus accumbens of enriched and isolated rats and the proteomic response to cocaine self-administration using a liquid chromatography mass spectrometry (LCMS) technique to quantify 1917 proteins. Results of complementary Ingenuity Pathways Analyses (IPA) and gene set enrichment analyses (GSEA), both performed using protein quantitative data, demonstrate that cocaine increases vesicular transporters for dopamine and glutamate as well as increasing proteins in the RhoA pathway. Further, cocaine regulates proteins related to ERK, CREB and AKT signaling. Environmental enrichment altered expression of a large number of proteins implicated in a diverse number of neuronal functions (e.g., energy production, mRNA splicing, and ubiquitination), molecular cascades (e.g., protein kinases), psychiatric disorders (e.g., mood disorders), and neurodegenerative diseases (e.g., Huntington's and Alzheimer's diseases). Upregulation of energy metabolism components in EC rats was verified using RNA sequencing. Most of the biological functions and pathways listed above were also identified in the Cocaine X Enrichment interaction analysis, providing clear evidence that enriched and isolated rats respond quite differently to cocaine exposure. The overall impression of the current results is that enriched saline-administering rats have a unique proteomic complement compared to enriched cocaine-administering rats as well as saline and cocaine-taking isolated rats. These results identify possible mechanisms of the protective phenotype and provide fertile soil for developing novel pharmacotherapeutics. Proteomics data are available via ProteomeXchange with identifier PXD000990.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:25100957
locator
sections[8] "Proteomic data analysis" paragraph 2
quote
The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:25100957
locator
sections[35] "Acknowledgments" paragraph 2
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
The headline result was that cocaine increased vesicular dopamine and glutamate transporters and proteins in the RhoA pathway, while environmental enrichment broadly altered the nucleus accumbens proteome; statistical inference used complementary IPA and protein-based GSEA, and the proteomics source data are available through ProteomeXchange identifier PXD000990.
steps array · 3 items
[0] object · 13 fields
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 object · 0 fields
inputs array · 1 item
[0]
source:pmid:25100957
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
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 · 1 item
[0]
data:geo:PXD000990
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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 object · 0 fields
inputs array · 1 item
[0]
data:geo:PXD000990
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 · 0 items
data object · 3 fields
state
partial
assets array · 6 items
[0] object · 15 fields
id
source:pmid:25100957
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fnbeh.2014.00246
sha256
sha256:fd61fe51b268529eed20a07508cdebf3762cb3172464720913025a316f995803
bytes
60814
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fnbeh.2014.00246
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
PMC4104784
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD000990
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD000990
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD000990
version
null
note
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
Cocaine and Environmental Enrichment Proteomics Study of Rat Nucleus Accumbens
resolution_checked_at
2026-10-31T18:35:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:25100957:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:26944538e00c3517a30fb22e8b5b957323991ec2f3c5d9dcfaccbe2ee5a27fa7
bytes
2482
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[11]/table-wrap[1]#T1
version
null
note
A selection of significantly changed proteins (p < 0.05; fold change > 1.5) for cocaine main effect, environmental enrichment main effect and cocaine X enrichment interaction.
structure object · 5 fields
pmcid
PMC4104784
section_index
11
section_title
Results
row_count
26
column_count
12
table object · 8 fields
label
Table 1
caption
A selection of significantly changed proteins (p < 0.05; fold change > 1.5) for cocaine main effect, environmental enrichment main effect and cocaine X enrichment interaction.
rows array · 26 items
[0] array · 12 items
[0]
Accession
[1]
Gene symbol
[2]
EC log2-fold
[3]
EC est fold
[4]
EC p-value
[5]
Coc log2-fold
[6]
Coc est fold
[7]
Coc p-value
[8]
Interaction log2 effect size
[9]
Interaction effect size
[10]
Interaction p-value
[11]
Fraction
[1] array · 12 items
[0]
P61751
[1]
ARF4
[2]
−2.21
[3]
−4.63
[4]
0.013
[5]
−1.39
[6]
−2.61
[7]
0.022
[8]
2.60
[9]
6.06
[10]
0.016
[11]
S1
[2] array · 12 items
[0]
Q1WIM2
[1]
CADM2
[2]
[3]
[4]
[5]
[6]
[7]
[8]
−0.61
[9]
−1.53
[10]
0.033
[11]
S1
[3] array · 12 items
[0]
Q5I0K3
[1]
CLYBL
[2]
[3]
[4]
[5]
2.02
[6]
4.05
[7]
0.036
[8]
[9]
[10]
[11]
S1
[4] array · 12 items
[0]
Q64611
[1]
CSAD
[2]
−5.30
[3]
−39.50
[4]
0.020
[5]
−4.41
[6]
−21.27
[7]
0.031
[8]
7.21
[9]
148.14
[10]
0.021
[11]
S1
[5] array · 12 items
[0]
P24268
[1]
CTSD
[2]
1.32
[3]
2.49
[4]
0.035
[5]
1.15
[6]
2.22
[7]
0.047
[8]
−1.59
[9]
−3.00
[10]
0.050
[11]
S1
[6] array · 12 items
[0]
Q9JHL4
[1]
DBNL
[2]
[3]
[4]
[5]
−0.33
[6]
−1.25
[7]
0.020
[8]
0.42
[9]
1.34
[10]
0.023
[11]
S1
[7] array · 12 items
[0]
Q641Y8
[1]
DDX1
[2]
−0.62
[3]
−1.54
[4]
0.020
[5]
[6]
[7]
[8]
0.89
[9]
1.86
[10]
0.020
[11]
S1
[8] array · 12 items
[0]
Q63622
[1]
DLG2
[2]
1.62
[3]
3.08
[4]
0.033
[5]
1.60
[6]
3.03
[7]
0.033
[8]
−2.17
[9]
−4.49
[10]
0.036
[11]
S1
[9] array · 12 items
[0]
Q6PDL0
[1]
DYNC1LI2
[2]
1.50
[3]
2.82
[4]
0.043
[5]
1.50
[6]
2.82
[7]
0.043
[8]
−2.09
[9]
−4.25
[10]
0.044
[11]
S1
[10] array · 12 items
[0]
Q8BGY2
[1]
EIF5A2
[2]
1.10
[3]
2.15
[4]
0.045
[5]
[6]
[7]
[8]
−1.37
[9]
−2.59
[10]
0.047
[11]
P1
[11] array · 12 items
[0]
O54921
[1]
EXOC2
[2]
1.77
[3]
3.41
[4]
0.033
[5]
1.67
[6]
3.18
[7]
0.036
[8]
−2.27
[9]
−4.82
[10]
0.040
[11]
S1
[12] array · 12 items
[0]
P28741
[1]
KIF3A
[2]
2.23
[3]
4.68
[4]
0.043
[5]
2.25
[6]
4.76
[7]
0.042
[8]
[9]
[10]
[11]
S1
[13] array · 12 items
[0]
P17046
[1]
LAMP2
[2]
[3]
[4]
[5]
3.40
[6]
10.56
[7]
0.041
[8]
[9]
[10]
[11]
S1
[14] array · 12 items
[0]
P21396
[1]
MAOA
[2]
0.82
[3]
1.76
[4]
0.047
[5]
[6]
[7]
[8]
[9]
[10]
[11]
P1
[15] array · 12 items
[0]
P36506
[1]
MAP2K2
[2]
−2.25
[3]
−4.74
[4]
0.018
[5]
[6]
[7]
[8]
2.65
[9]
6.26
[10]
0.022
[11]
S1
[16] array · 12 items
[0]
P10637
[1]
MAPT
[2]
1.22
[3]
2.33
[4]
0.045
[5]
[6]
[7]
[8]
[9]
[10]
[11]
P1
[17] array · 12 items
[0]
Q69ZK9
[1]
NLGN2
[2]
[3]
[4]
[5]
[6]
[7]
[8]
−0.93
[9]
−1.90
[10]
0.048
[11]
S1
[18] array · 12 items
[0]
Q6PEC4
[1]
SKP1
[2]
[3]
[4]
[5]
[6]
[7]
[8]
0.91
[9]
1.88
[10]
0.032
[11]
S1
[19] array · 12 items
[0]
Q9JI12
[1]
SLC17A6
[2]
[3]
[4]
[5]
4.58
[6]
23.87
[7]
0.033
[8]
[9]
[10]
[11]
S1
[20] array · 12 items
[0]
Q62634
[1]
SLC17A7
[2]
[3]
[4]
[5]
4.55
[6]
23.43
[7]
0.031
[8]
[9]
[10]
[11]
S1
[21] array · 12 items
[0]
Q8BRU6
[1]
SLC18A2
[2]
[3]
[4]
[5]
0.93
[6]
1.91
[7]
0.044
[8]
[9]
[10]
[11]
S1
[22] array · 12 items
[0]
Q80ZA5
[1]
SLC4A10
[2]
3.02
[3]
8.10
[4]
0.021
[5]
3.63
[6]
12.37
[7]
0.018
[8]
−3.99
[9]
−15.90
[10]
0.024
[11]
S1
[23] array · 12 items
[0]
P07895
[1]
SOD2
[2]
0.91
[3]
1.88
[4]
0.049
[5]
[6]
[7]
[8]
[9]
[10]
[11]
S1
[24] array · 12 items
[0]
Q9CQN6
[1]
TMEM14C
[2]
[3]
[4]
[5]
2.97
[6]
7.84
[7]
0.036
[8]
[9]
[10]
[11]
S1
[25] array · 12 items
[0]
Q60930
[1]
VDAC2
[2]
0.68
[3]
1.61
[4]
0.030
[5]
[6]
[7]
[8]
[9]
[10]
[11]
P1
row_count
26
column_count
12
numeric_cells
154
header_rows
1
locator
section[11]/table-wrap[1]#T1
[3] object · 16 fields
id
asset:table:pmid:25100957:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:adeab2ea880e0ba7fcad7c184b77bb3a26626e2bda95a7562072da48987e3e6c
bytes
1401
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[13]/table-wrap[1]#T2
version
null
note
A selection of cocaine-regulated protein sets from the GSEA analysis.
structure object · 5 fields
pmcid
PMC4104784
section_index
13
section_title
Confirmatory evidence
row_count
18
column_count
6
table object · 8 fields
label
Table 2
caption
A selection of cocaine-regulated protein sets from the GSEA analysis.
rows array · 18 items
[0] array · 6 items
[0]
[1]
MSigDB collection
[2]
Proteins
[3]
Enrichment score
[4]
NES
[5]
p-value
[1] array · 1 item
[0]
DOWNREGULATED BY COCAINE
[2] array · 6 items
[0]
MITOCHONDRIAL_ENVELOPE
[1]
C5
[2]
51
[3]
0.61
[4]
2.08
[5]
0.001
[3] array · 6 items
[0]
REACTOME_TCA_CYCLE_AND_RESPIRATORY ELECTRON_TRANSPORT
[1]
C2
[2]
82
[3]
0.53
[4]
1.91
[5]
0.001
[4] array · 6 items
[0]
KEGG_PARKINSONS_DISEASE
[1]
C2
[2]
65
[3]
0.51
[4]
1.77
[5]
0.001
[5] array · 6 items
[0]
KEGG_ALZHEIMERS_DISEASE
[1]
C2
[2]
68
[3]
0.49
[4]
1.77
[5]
0.001
[6] array · 6 items
[0]
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT
[1]
C2
[2]
44
[3]
0.48
[4]
1.59
[5]
0.006
[7] array · 6 items
[0]
KEGG_HUNTINGTONS_DISEASE
[1]
C2
[2]
75
[3]
0.43
[4]
1.57
[5]
0.001
[8] array · 6 items
[0]
ANTI_APOPTOSIS
[1]
C5
[2]
21
[3]
0.56
[4]
1.55
[5]
0.034
[9] array · 1 item
[0]
UPREGULATED BY COCAINE
[10] array · 6 items
[0]
PID_ER_NONGENOMIC_PATHWAY
[1]
C2
[2]
19
[3]
−0.79
[4]
−1.94
[5]
0.001
[11] array · 6 items
[0]
ST_INTEGRIN_SIGNALING_PATHWAY
[1]
C2
[2]
20
[3]
−0.78
[4]
−1.93
[5]
0.005
[12] array · 6 items
[0]
PID_RHOA_PATHWAY
[1]
C2
[2]
17
[3]
−0.77
[4]
−1.82
[5]
0.003
[13] array · 6 items
[0]
PROTEIN_SERINE_THREONINE_KINASE_ACTIVITY
[1]
C5
[2]
25
[3]
−0.69
[4]
−1.78
[5]
0.005
[14] array · 6 items
[0]
KEGG_WNT_SIGNALING_PATHWAY
[1]
C2
[2]
28
[3]
−0.67
[4]
−1.74
[5]
0.005
[15] array · 6 items
[0]
SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON BY_RHO_GTPASES
[1]
C2
[2]
17
[3]
−0.73
[4]
−1.67
[5]
0.012
[16] array · 6 items
[0]
KEGG_CHEMOKINE_SIGNALING_PATHWAY
[1]
C2
[2]
28
[3]
−0.64
[4]
−1.64
[5]
0.010
[17] array · 6 items
[0]
REACTOME_SEMAPHORIN_INTERACTIONS
[1]
C2
[2]
25
[3]
−0.62
[4]
−1.60
[5]
0.021
row_count
18
column_count
6
numeric_cells
60
header_rows
1
locator
section[13]/table-wrap[1]#T2
[4] object · 16 fields
id
asset:table:pmid:25100957:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:adeab2ea880e0ba7fcad7c184b77bb3a26626e2bda95a7562072da48987e3e6c
bytes
1401
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[13]/table-wrap[1]#T2
version
null
note
A selection of cocaine-regulated protein sets from the GSEA analysis.
structure object · 5 fields
pmcid
PMC4104784
section_index
18
section_title
Confirmatory evidence
row_count
18
column_count
6
table object · 8 fields
label
Table 2
caption
A selection of cocaine-regulated protein sets from the GSEA analysis.
rows array · 18 items
[0] array · 6 items
[0]
[1]
MSigDB collection
[2]
Proteins
[3]
Enrichment score
[4]
NES
[5]
p-value
[1] array · 1 item
[0]
DOWNREGULATED BY COCAINE
[2] array · 6 items
[0]
MITOCHONDRIAL_ENVELOPE
[1]
C5
[2]
51
[3]
0.61
[4]
2.08
[5]
0.001
[3] array · 6 items
[0]
REACTOME_TCA_CYCLE_AND_RESPIRATORY ELECTRON_TRANSPORT
[1]
C2
[2]
82
[3]
0.53
[4]
1.91
[5]
0.001
[4] array · 6 items
[0]
KEGG_PARKINSONS_DISEASE
[1]
C2
[2]
65
[3]
0.51
[4]
1.77
[5]
0.001
[5] array · 6 items
[0]
KEGG_ALZHEIMERS_DISEASE
[1]
C2
[2]
68
[3]
0.49
[4]
1.77
[5]
0.001
[6] array · 6 items
[0]
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT
[1]
C2
[2]
44
[3]
0.48
[4]
1.59
[5]
0.006
[7] array · 6 items
[0]
KEGG_HUNTINGTONS_DISEASE
[1]
C2
[2]
75
[3]
0.43
[4]
1.57
[5]
0.001
[8] array · 6 items
[0]
ANTI_APOPTOSIS
[1]
C5
[2]
21
[3]
0.56
[4]
1.55
[5]
0.034
[9] array · 1 item
[0]
UPREGULATED BY COCAINE
[10] array · 6 items
[0]
PID_ER_NONGENOMIC_PATHWAY
[1]
C2
[2]
19
[3]
−0.79
[4]
−1.94
[5]
0.001
[11] array · 6 items
[0]
ST_INTEGRIN_SIGNALING_PATHWAY
[1]
C2
[2]
20
[3]
−0.78
[4]
−1.93
[5]
0.005
[12] array · 6 items
[0]
PID_RHOA_PATHWAY
[1]
C2
[2]
17
[3]
−0.77
[4]
−1.82
[5]
0.003
[13] array · 6 items
[0]
PROTEIN_SERINE_THREONINE_KINASE_ACTIVITY
[1]
C5
[2]
25
[3]
−0.69
[4]
−1.78
[5]
0.005
[14] array · 6 items
[0]
KEGG_WNT_SIGNALING_PATHWAY
[1]
C2
[2]
28
[3]
−0.67
[4]
−1.74
[5]
0.005
[15] array · 6 items
[0]
SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON BY_RHO_GTPASES
[1]
C2
[2]
17
[3]
−0.73
[4]
−1.67
[5]
0.012
[16] array · 6 items
[0]
KEGG_CHEMOKINE_SIGNALING_PATHWAY
[1]
C2
[2]
28
[3]
−0.64
[4]
−1.64
[5]
0.010
[17] array · 6 items
[0]
REACTOME_SEMAPHORIN_INTERACTIONS
[1]
C2
[2]
25
[3]
−0.62
[4]
−1.60
[5]
0.021
row_count
18
column_count
6
numeric_cells
60
header_rows
1
locator
section[13]/table-wrap[1]#T2
[5] object · 16 fields
id
asset:table:pmid:25100957:4
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:0ac17246703690900467d98f0c399fe3d57e2c2678f10293f0c74f778f1056e2
bytes
1552
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[20]/table-wrap[1]#T3
version
null
note
A selection of environmental enrichment-regulated protein sets from the GSEA analysis.
structure object · 5 fields
pmcid
PMC4104784
section_index
20
section_title
Splicing and mRNA processing
row_count
21
column_count
6
table object · 8 fields
label
Table 3
caption
A selection of environmental enrichment-regulated protein sets from the GSEA analysis.
rows array · 21 items
[0] array · 6 items
[0]
[1]
MSigDB collection
[2]
Proteins
[3]
Enrichment score
[4]
NES
[5]
p-value
[1] array · 1 item
[0]
DOWNREGULATED IN EC
[2] array · 6 items
[0]
RIBONUCLEOPROTEIN_COMPLEX
[1]
C5
[2]
42
[3]
−0.69
[4]
−2.28
[5]
0.001
[3] array · 6 items
[0]
KEGG_SPLICEOSOME
[1]
C2
[2]
45
[3]
−0.65
[4]
−2.14
[5]
0.001
[4] array · 6 items
[0]
PID_MTOR_4PATHWAY
[1]
C2
[2]
22
[3]
−0.66
[4]
−1.86
[5]
0.003
[5] array · 6 items
[0]
KOYAMA_SEMA3B_TARGETS_UP
[1]
C2
[2]
20
[3]
−0.62
[4]
−1.71
[5]
0.005
[6] array · 6 items
[0]
TRANSMEMBRANE_RECEPTOR_ACTIVITY
[1]
C5
[2]
16
[3]
−0.59
[4]
−1.53
[5]
0.056
[7] array · 1 item
[0]
UPREGULATED IN EC
[8] array · 6 items
[0]
REACTOME_TCA_CYCLE_AND_RESPIRATORY ELECTRON_TRANSPORT
[1]
C2
[2]
82
[3]
0.57
[4]
1.96
[5]
0.001
[9] array · 6 items
[0]
KEGG_PARKINSONS_DISEASE
[1]
C2
[2]
65
[3]
0.56
[4]
1.84
[5]
0.001
[10] array · 6 items
[0]
KEGG_HUNTINGTONS_DISEASE
[1]
C2
[2]
75
[3]
0.53
[4]
1.78
[5]
0.001
[11] array · 6 items
[0]
KEGG_ALZHEIMERS_DISEASE
[1]
C2
[2]
68
[3]
0.54
[4]
1.77
[5]
0.001
[12] array · 6 items
[0]
SUBSTRATE_SPECIFIC_TRANSPORTER_ACTIVITY
[1]
C5
[2]
57
[3]
0.54
[4]
1.74
[5]
0.001
[13] array · 6 items
[0]
KEGG_GLYCOLYSIS_GLUCONEOGENESIS
[1]
C2
[2]
28
[3]
0.63
[4]
1.73
[5]
0.002
[14] array · 6 items
[0]
ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY
[1]
C5
[2]
25
[3]
0.64
[4]
1.72
[5]
0.003
[15] array · 6 items
[0]
PROTEIN_KINASE_CASCADE
[1]
C5
[2]
30
[3]
0.60
[4]
1.69
[5]
0.003
[16] array · 6 items
[0]
REACTOME_SIGNALING_BY_RHO_GTPASES
[1]
C2
[2]
20
[3]
0.62
[4]
1.66
[5]
0.010
[17] array · 6 items
[0]
NEGATIVE_REGULATION_OF_APOPTOSIS
[1]
C5
[2]
29
[3]
0.58
[4]
1.62
[5]
0.012
[18] array · 6 items
[0]
STEIN_ESRRA_TARGETS_UP
[1]
C2
[2]
107
[3]
0.45
[4]
1.60
[5]
0.001
[19] array · 6 items
[0]
PHOSPHOPROTEIN_PHOSPHATASE_ACTIVITY
[1]
C5
[2]
18
[3]
0.62
[4]
1.54
[5]
0.026
[20] array · 6 items
[0]
NEUROGENESIS
[1]
C5
[2]
23
[3]
0.56
[4]
1.52
[5]
0.025
row_count
21
column_count
6
numeric_cells
73
header_rows
1
locator
section[20]/table-wrap[1]#T3
gaps array · 2 items
[0]
asset:data:geo:PXD000990 not downloaded
[1]
asset:data:geo:PXD000990 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
expressible
true
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).
targets array · 0 items
gaps array · 0 items
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
R1
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocking_axis
none
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
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: anova.
capability object · 4 fields
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 object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
PXD000990
resolved_accessions array · 1 item
[0]
PXD000990
statements array · 1 item
[0]
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.
basis
The paper names PXD000990 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 6 items
[0]
source:pmid:25100957
[1]
data:geo:PXD000990
[2]
asset:table:pmid:25100957:1
[3]
asset:table:pmid:25100957:2
[4]
asset:table:pmid:25100957:3
[5]
asset:table:pmid:25100957:4
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:PXD000990
gaps array · 0 items
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
2026-10-31T18:22:39Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
125041
completion_tokens
3996
cached_tokens
93434
human_critique
null
stages array · 1 item
[0] object · 4 fields
id
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
id
pmid:25100957
type
paper
label
pmid:25100957
[1] object · 3 fields
id
source:pmid:25100957
type
manuscript
label
PMID 25100957 full text
[2] object · 3 fields
id
data:geo:PXD000990
type
dataset
label
GEO PXD000990
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:25100957
type
paper
label
pmid:25100957
[1] object · 3 fields
id
source:pmid:25100957
type
manuscript
label
PMID 25100957 full text
[2] object · 3 fields
id
data:geo:PXD000990
type
dataset
label
GEO PXD000990
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-25100957
type
extraction
used array · 1 item
[0]
source:pmid:25100957
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD000990
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD000990
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
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 object · 4 fields
parent_id
pmid:25100957
parent_hash
sha256:99b22c317c067c330883d9d3530f8b4a36f050ebdae40c92f9cb3b41f2255fff
fork_of
null
generation
7
gaps array · 6 items
[0]
asset:data:geo:PXD000990 licence not read
[1]
asset:data:geo:PXD000990 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
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]
well as the proteomic response to cocaine in rat nucleus accumbens.
[1]
leading to a protective addiction phenotype in rats. Understanding the mechanisms underlying thi
[2]
ading to a protective addiction phenotype in rats. Understanding the mechanisms underlying thi
[3]
e nucleus accumbens of enriched and isolated rats and the proteomic response to cocaine self-a
order_basis
paper_text_order:54
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
rna_seq
definition_version
99e1195c7d6f
definition_digest
null
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
ism components in EC rats was verified using RNA sequencing. Most of the biological functions and pathwa
order_basis
paper_text_order:1426
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
definition_digest
null
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
confidence
1
evidence array · 1 item
[0]
The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).
order_basis
consumes_earlier_output
id
assay:3
Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25100957", "kind": "science-record", "revision": 8, "content_hash": "sha256:91eb50c3d2b07e015c07c93eb0c6ef65165411917fe6cab435228cb02d243d18", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T22:42:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Environmental enrichment alters protein expression as well as the proteomic response to cocaine in rat nucleus accumbens.", "doi": "10.3389/fnbeh.2014.00246", "pmid": "25100957", "authors": ["Cheryl F Lichti", "Xiuzhen Fan", "Robert D English", "Yafang Zhang", "Dingge Li", "Fanping Kong", "Mala Sinha", "Clark R Andersen", "Heidi Spratt", "Bruce A Luxon", "Thomas A Green"], "journal": "Frontiers in behavioral neuroscience", "year": 2014, "abstract": "Prior research demonstrated that environmental enrichment creates individual differences in behavior leading to a protective addiction phenotype in rats. Understanding the mechanisms underlying this phenotype will guide selection of targets for much-needed novel pharmacotherapeutics. The current study investigates differences in proteome expression in the nucleus accumbens of enriched and isolated rats and the proteomic response to cocaine self-administration using a liquid chromatography mass spectrometry (LCMS) technique to quantify 1917 proteins. Results of complementary Ingenuity Pathways Analyses (IPA) and gene set enrichment analyses (GSEA), both performed using protein quantitative data, demonstrate that cocaine increases vesicular transporters for dopamine and glutamate as well as increasing proteins in the RhoA pathway. Further, cocaine regulates proteins related to ERK, CREB and AKT signaling. Environmental enrichment altered expression of a large number of proteins implicated in a diverse number of neuronal functions (e.g., energy production, mRNA splicing, and ubiquitination), molecular cascades (e.g., protein kinases), psychiatric disorders (e.g., mood disorders), and neurodegenerative diseases (e.g., Huntington's and Alzheimer's diseases). Upregulation of energy metabolism components in EC rats was verified using RNA sequencing. Most of the biological functions and pathways listed above were also identified in the Cocaine X Enrichment interaction analysis, providing clear evidence that enriched and isolated rats respond quite differently to cocaine exposure. The overall impression of the current results is that enriched saline-administering rats have a unique proteomic complement compared to enriched cocaine-administering rats as well as saline and cocaine-taking isolated rats. These results identify possible mechanisms of the protective phenotype and provide fertile soil for developing novel pharmacotherapeutics. Proteomics data are available via ProteomeXchange with identifier PXD000990.", "claims": [{"id": "claim-method", "statement": "The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25100957", "locator": "sections[8] \"Proteomic data analysis\" paragraph 2", "quote": "The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25100957", "locator": "sections[35] \"Acknowledgments\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The headline result was that cocaine increased vesicular dopamine and glutamate transporters and proteins in the RhoA pathway, while environmental enrichment broadly altered the nucleus accumbens proteome; statistical inference used complementary IPA and protein-based GSEA, and the proteomics source data are available through ProteomeXchange identifier PXD000990.", "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:25100957"], "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": "complete", "blocked_on": null, "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": ["data:geo:PXD000990"], "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": ["data:geo:PXD000990"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25100957", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnbeh.2014.00246", "sha256": "sha256:fd61fe51b268529eed20a07508cdebf3762cb3172464720913025a316f995803", "bytes": 60814, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnbeh.2014.00246", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4104784", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000990", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD000990", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000990", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Cocaine and Environmental Enrichment Proteomics Study of Rat Nucleus Accumbens", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:25100957:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:26944538e00c3517a30fb22e8b5b957323991ec2f3c5d9dcfaccbe2ee5a27fa7", "bytes": 2482, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T1", "version": null, "note": "A selection of significantly changed proteins (p < 0.05; fold change > 1.5) for cocaine main effect, environmental enrichment main effect and cocaine X enrichment interaction.", "structure": {"pmcid": "PMC4104784", "section_index": 11, "section_title": "Results", "row_count": 26, "column_count": 12}, "table": {"label": "Table 1", "caption": "A selection of significantly changed proteins (p < 0.05; fold change > 1.5) for cocaine main effect, environmental enrichment main effect and cocaine X enrichment interaction.", "rows": [["Accession", "Gene symbol", "EC log2-fold", "EC est fold", "EC p-value", "Coc log2-fold", "Coc est fold", "Coc p-value", "Interaction log2 effect size", "Interaction effect size", "Interaction p-value", "Fraction"], ["P61751", "ARF4", "−2.21", "−4.63", "0.013", "−1.39", "−2.61", "0.022", "2.60", "6.06", "0.016", "S1"], ["Q1WIM2", "CADM2", "", "", "", "", "", "", "−0.61", "−1.53", "0.033", "S1"], ["Q5I0K3", "CLYBL", "", "", "", "2.02", "4.05", "0.036", "", "", "", "S1"], ["Q64611", "CSAD", "−5.30", "−39.50", "0.020", "−4.41", "−21.27", "0.031", "7.21", "148.14", "0.021", "S1"], ["P24268", "CTSD", "1.32", "2.49", "0.035", "1.15", "2.22", "0.047", "−1.59", "−3.00", "0.050", "S1"], ["Q9JHL4", "DBNL", "", "", "", "−0.33", "−1.25", "0.020", "0.42", "1.34", "0.023", "S1"], ["Q641Y8", "DDX1", "−0.62", "−1.54", "0.020", "", "", "", "0.89", "1.86", "0.020", "S1"], ["Q63622", "DLG2", "1.62", "3.08", "0.033", "1.60", "3.03", "0.033", "−2.17", "−4.49", "0.036", "S1"], ["Q6PDL0", "DYNC1LI2", "1.50", "2.82", "0.043", "1.50", "2.82", "0.043", "−2.09", "−4.25", "0.044", "S1"], ["Q8BGY2", "EIF5A2", "1.10", "2.15", "0.045", "", "", "", "−1.37", "−2.59", "0.047", "P1"], ["O54921", "EXOC2", "1.77", "3.41", "0.033", "1.67", "3.18", "0.036", "−2.27", "−4.82", "0.040", "S1"], ["P28741", "KIF3A", "2.23", "4.68", "0.043", "2.25", "4.76", "0.042", "", "", "", "S1"], ["P17046", "LAMP2", "", "", "", "3.40", "10.56", "0.041", "", "", "", "S1"], ["P21396", "MAOA", "0.82", "1.76", "0.047", "", "", "", "", "", "", "P1"], ["P36506", "MAP2K2", "−2.25", "−4.74", "0.018", "", "", "", "2.65", "6.26", "0.022", "S1"], ["P10637", "MAPT", "1.22", "2.33", "0.045", "", "", "", "", "", "", "P1"], ["Q69ZK9", "NLGN2", "", "", "", "", "", "", "−0.93", "−1.90", "0.048", "S1"], ["Q6PEC4", "SKP1", "", "", "", "", "", "", "0.91", "1.88", "0.032", "S1"], ["Q9JI12", "SLC17A6", "", "", "", "4.58", "23.87", "0.033", "", "", "", "S1"], ["Q62634", "SLC17A7", "", "", "", "4.55", "23.43", "0.031", "", "", "", "S1"], ["Q8BRU6", "SLC18A2", "", "", "", "0.93", "1.91", "0.044", "", "", "", "S1"], ["Q80ZA5", "SLC4A10", "3.02", "8.10", "0.021", "3.63", "12.37", "0.018", "−3.99", "−15.90", "0.024", "S1"], ["P07895", "SOD2", "0.91", "1.88", "0.049", "", "", "", "", "", "", "S1"], ["Q9CQN6", "TMEM14C", "", "", "", "2.97", "7.84", "0.036", "", "", "", "S1"], ["Q60930", "VDAC2", "0.68", "1.61", "0.030", "", "", "", "", "", "", "P1"]], "row_count": 26, "column_count": 12, "numeric_cells": 154, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:25100957:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:adeab2ea880e0ba7fcad7c184b77bb3a26626e2bda95a7562072da48987e3e6c", "bytes": 1401, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T2", "version": null, "note": "A selection of cocaine-regulated protein sets from the GSEA analysis.", "structure": {"pmcid": "PMC4104784", "section_index": 13, "section_title": "Confirmatory evidence", "row_count": 18, "column_count": 6}, "table": {"label": "Table 2", "caption": "A selection of cocaine-regulated protein sets from the GSEA analysis.", "rows": [["", "MSigDB collection", "Proteins", "Enrichment score", "NES", "p-value"], ["DOWNREGULATED BY COCAINE"], ["MITOCHONDRIAL_ENVELOPE", "C5", "51", "0.61", "2.08", "0.001"], ["REACTOME_TCA_CYCLE_AND_RESPIRATORY ELECTRON_TRANSPORT", "C2", "82", "0.53", "1.91", "0.001"], ["KEGG_PARKINSONS_DISEASE", "C2", "65", "0.51", "1.77", "0.001"], ["KEGG_ALZHEIMERS_DISEASE", "C2", "68", "0.49", "1.77", "0.001"], ["REACTOME_RESPIRATORY_ELECTRON_TRANSPORT", "C2", "44", "0.48", "1.59", "0.006"], ["KEGG_HUNTINGTONS_DISEASE", "C2", "75", "0.43", "1.57", "0.001"], ["ANTI_APOPTOSIS", "C5", "21", "0.56", "1.55", "0.034"], ["UPREGULATED BY COCAINE"], ["PID_ER_NONGENOMIC_PATHWAY", "C2", "19", "−0.79", "−1.94", "0.001"], ["ST_INTEGRIN_SIGNALING_PATHWAY", "C2", "20", "−0.78", "−1.93", "0.005"], ["PID_RHOA_PATHWAY", "C2", "17", "−0.77", "−1.82", "0.003"], ["PROTEIN_SERINE_THREONINE_KINASE_ACTIVITY", "C5", "25", "−0.69", "−1.78", "0.005"], ["KEGG_WNT_SIGNALING_PATHWAY", "C2", "28", "−0.67", "−1.74", "0.005"], ["SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON BY_RHO_GTPASES", "C2", "17", "−0.73", "−1.67", "0.012"], ["KEGG_CHEMOKINE_SIGNALING_PATHWAY", "C2", "28", "−0.64", "−1.64", "0.010"], ["REACTOME_SEMAPHORIN_INTERACTIONS", "C2", "25", "−0.62", "−1.60", "0.021"]], "row_count": 18, "column_count": 6, "numeric_cells": 60, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:25100957:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:adeab2ea880e0ba7fcad7c184b77bb3a26626e2bda95a7562072da48987e3e6c", "bytes": 1401, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T2", "version": null, "note": "A selection of cocaine-regulated protein sets from the GSEA analysis.", "structure": {"pmcid": "PMC4104784", "section_index": 18, "section_title": "Confirmatory evidence", "row_count": 18, "column_count": 6}, "table": {"label": "Table 2", "caption": "A selection of cocaine-regulated protein sets from the GSEA analysis.", "rows": [["", "MSigDB collection", "Proteins", "Enrichment score", "NES", "p-value"], ["DOWNREGULATED BY COCAINE"], ["MITOCHONDRIAL_ENVELOPE", "C5", "51", "0.61", "2.08", "0.001"], ["REACTOME_TCA_CYCLE_AND_RESPIRATORY ELECTRON_TRANSPORT", "C2", "82", "0.53", "1.91", "0.001"], ["KEGG_PARKINSONS_DISEASE", "C2", "65", "0.51", "1.77", "0.001"], ["KEGG_ALZHEIMERS_DISEASE", "C2", "68", "0.49", "1.77", "0.001"], ["REACTOME_RESPIRATORY_ELECTRON_TRANSPORT", "C2", "44", "0.48", "1.59", "0.006"], ["KEGG_HUNTINGTONS_DISEASE", "C2", "75", "0.43", "1.57", "0.001"], ["ANTI_APOPTOSIS", "C5", "21", "0.56", "1.55", "0.034"], ["UPREGULATED BY COCAINE"], ["PID_ER_NONGENOMIC_PATHWAY", "C2", "19", "−0.79", "−1.94", "0.001"], ["ST_INTEGRIN_SIGNALING_PATHWAY", "C2", "20", "−0.78", "−1.93", "0.005"], ["PID_RHOA_PATHWAY", "C2", "17", "−0.77", "−1.82", "0.003"], ["PROTEIN_SERINE_THREONINE_KINASE_ACTIVITY", "C5", "25", "−0.69", "−1.78", "0.005"], ["KEGG_WNT_SIGNALING_PATHWAY", "C2", "28", "−0.67", "−1.74", "0.005"], ["SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON BY_RHO_GTPASES", "C2", "17", "−0.73", "−1.67", "0.012"], ["KEGG_CHEMOKINE_SIGNALING_PATHWAY", "C2", "28", "−0.64", "−1.64", "0.010"], ["REACTOME_SEMAPHORIN_INTERACTIONS", "C2", "25", "−0.62", "−1.60", "0.021"]], "row_count": 18, "column_count": 6, "numeric_cells": 60, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:25100957:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0ac17246703690900467d98f0c399fe3d57e2c2678f10293f0c74f778f1056e2", "bytes": 1552, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#T3", "version": null, "note": "A selection of environmental enrichment-regulated protein sets from the GSEA analysis.", "structure": {"pmcid": "PMC4104784", "section_index": 20, "section_title": "Splicing and mRNA processing", "row_count": 21, "column_count": 6}, "table": {"label": "Table 3", "caption": "A selection of environmental enrichment-regulated protein sets from the GSEA analysis.", "rows": [["", "MSigDB collection", "Proteins", "Enrichment score", "NES", "p-value"], ["DOWNREGULATED IN EC"], ["RIBONUCLEOPROTEIN_COMPLEX", "C5", "42", "−0.69", "−2.28", "0.001"], ["KEGG_SPLICEOSOME", "C2", "45", "−0.65", "−2.14", "0.001"], ["PID_MTOR_4PATHWAY", "C2", "22", "−0.66", "−1.86", "0.003"], ["KOYAMA_SEMA3B_TARGETS_UP", "C2", "20", "−0.62", "−1.71", "0.005"], ["TRANSMEMBRANE_RECEPTOR_ACTIVITY", "C5", "16", "−0.59", "−1.53", "0.056"], ["UPREGULATED IN EC"], ["REACTOME_TCA_CYCLE_AND_RESPIRATORY ELECTRON_TRANSPORT", "C2", "82", "0.57", "1.96", "0.001"], ["KEGG_PARKINSONS_DISEASE", "C2", "65", "0.56", "1.84", "0.001"], ["KEGG_HUNTINGTONS_DISEASE", "C2", "75", "0.53", "1.78", "0.001"], ["KEGG_ALZHEIMERS_DISEASE", "C2", "68", "0.54", "1.77", "0.001"], ["SUBSTRATE_SPECIFIC_TRANSPORTER_ACTIVITY", "C5", "57", "0.54", "1.74", "0.001"], ["KEGG_GLYCOLYSIS_GLUCONEOGENESIS", "C2", "28", "0.63", "1.73", "0.002"], ["ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY", "C5", "25", "0.64", "1.72", "0.003"], ["PROTEIN_KINASE_CASCADE", "C5", "30", "0.60", "1.69", "0.003"], ["REACTOME_SIGNALING_BY_RHO_GTPASES", "C2", "20", "0.62", "1.66", "0.010"], ["NEGATIVE_REGULATION_OF_APOPTOSIS", "C5", "29", "0.58", "1.62", "0.012"], ["STEIN_ESRRA_TARGETS_UP", "C2", "107", "0.45", "1.60", "0.001"], ["PHOSPHOPROTEIN_PHOSPHATASE_ACTIVITY", "C5", "18", "0.62", "1.54", "0.026"], ["NEUROGENESIS", "C5", "23", "0.56", "1.52", "0.025"]], "row_count": 21, "column_count": 6, "numeric_cells": 73, "header_rows": 1, "locator": "section[20]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:PXD000990 not downloaded", "asset:data:geo:PXD000990 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995)."}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": "R1", "reachable": true, "accessions": ["PXD000990"], "resolved_accessions": ["PXD000990"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al., 2014) with the dataset identifier PXD000990."], "basis": "The paper names PXD000990 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:25100957", "data:geo:PXD000990", "asset:table:pmid:25100957:1", "asset:table:pmid:25100957:2", "asset:table:pmid:25100957:3", "asset:table:pmid:25100957:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000990"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:39Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 125041, "completion_tokens": 3996, "cached_tokens": 93434}}, "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:25100957", "type": "paper", "label": "pmid:25100957"}, {"id": "source:pmid:25100957", "type": "manuscript", "label": "PMID 25100957 full text"}, {"id": "data:geo:PXD000990", "type": "dataset", "label": "GEO PXD000990"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25100957", "type": "paper", "label": "pmid:25100957"}, {"id": "source:pmid:25100957", "type": "manuscript", "label": "PMID 25100957 full text"}, {"id": "data:geo:PXD000990", "type": "dataset", "label": "GEO PXD000990"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25100957", "type": "extraction", "used": ["source:pmid:25100957"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000990", "type": "accession_resolution", "used": ["data:geo:PXD000990"], "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:25100957", "parent_hash": "sha256:99b22c317c067c330883d9d3530f8b4a36f050ebdae40c92f9cb3b41f2255fff", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD000990 licence not read", "asset:data:geo:PXD000990 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["well as the proteomic response to cocaine in rat nucleus accumbens.", "leading to a protective addiction phenotype in rats. Understanding the mechanisms underlying thi", "ading to a protective addiction phenotype in rats. Understanding the mechanisms underlying thi", "e nucleus accumbens of enriched and isolated rats and the proteomic response to cocaine self-a"], "order_basis": "paper_text_order:54", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ism components in EC rats was verified using RNA sequencing. Most of the biological functions and pathwa"], "order_basis": "paper_text_order:1426", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The resulting proteins were quantified by Two-Way ANOVA, and p-value adjustment was performed according to the Benjamini and Hochberg method (Benjamini and Hochberg, 1995)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}