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

pmid:31485792

Nervous NDRGs: the N-myc downstream-regulated gene family in the central and peripheral nervous system.

Simone L Schonkeren · Maartje Massen · Raisa van der Horst · Alexander Koch · Nathalie Vaes · Veerle Melotte

Neurogenetics · 2019 doi:10.1007/s10048-019-00587-0

Paper

complete

Experiment

complete

Data

partial

Analysis

absent

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
id
pmid:31485792
kind
science-record
content_hash
sha256:791b02eab42ce259b5ff78be5f83313bbcc7174994808a78f00ae5f99e5d29e4
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:49Z
updated_at
2026-11-01T18:51:14Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Nervous NDRGs: the N-myc downstream-regulated gene family in the central and peripheral nervous system.
doi
10.1007/s10048-019-00587-0
pmid
31485792
authors array · 6 items
[0]
Simone L Schonkeren
[1]
Maartje Massen
[2]
Raisa van der Horst
[3]
Alexander Koch
[4]
Nathalie Vaes
[5]
Veerle Melotte
journal
Neurogenetics
year
2019
abstract
The N-Myc downstream-regulated gene (NDRG) family consists of four members (NDRG1, NDRG2, NDRG3, NDRG4) that are differentially expressed in various organs and function in important processes, like cell proliferation and differentiation. In the last couple of decades, interest in this family has risen due to its connection with several disorders of the nervous system including Charcot-Marie-Tooth disease and dementia, as well as nervous system cancers. By combining a literature review with in silico data analysis of publicly available datasets, such as the Mouse Brain Atlas, BrainSpan, the Genotype-Tissue Expression (GTEx) project, and Gene Expression Omnibus (GEO) datasets, this review summarizes the expression and functions of the NDRG family in the healthy and diseased nervous system. We here show that the NDRGs have a differential, relatively cell type-specific, expression pattern in the nervous system. Even though NDRGs share functionalities, like a role in vesicle trafficking, stress response, and neurite outgrowth, other functionalities seem to be unique to a specific member, e.g., the role of NDRG1 in myelination. Furthermore, mutations, phosphorylation, or changes in expression of NDRGs are related to nervous system diseases, including peripheral neuropathy and different forms of dementia. Moreover, NDRG1, NDRG2, and NDRG4 are all involved in cancers of the nervous system, such as glioma, neuroblastoma, or meningioma. All in all, our review elucidates that although the NDRGs belong to the same gene family and share some functional features, they should be considered unique in their expression patterns and functional importance for nervous system development and neuronal diseases.
claims array · 1 item
[0] object · 6 fields
id
claim-data-access
statement
Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:31485792
locator
sections[3] "Cellular expression" paragraph 3
quote
Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:31485792
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE35366
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE35366
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 · 4 items
[0] object · 15 fields
id
source:pmid:31485792
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s10048-019-00587-0
sha256
sha256:dd14a11fd7ea2c4aaad42476f949d49cff8783a860f8e49f7fa40e5f1707c8c3
bytes
69450
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s10048-019-00587-0
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
PMC6754360
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE35366
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=GSE35366
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE35366
version
null
note
Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).
access_statement_kind
repository_route_statement
sample_accessions array · 78 items
[0]
GSM866834
[1]
GSM866835
[2]
GSM866836
[3]
GSM866837
[4]
GSM866838
[5]
GSM866839
[6]
GSM866840
[7]
GSM866841
[8]
GSM866842
[9]
GSM866843
[10]
GSM866844
[11]
GSM866845
[12]
GSM866846
[13]
GSM866847
[14]
GSM866848
[15]
GSM866849
[16]
GSM866850
[17]
GSM866851
[18]
GSM866852
[19]
GSM866853
[20]
GSM866854
[21]
GSM866855
[22]
GSM866856
[23]
GSM866857
[24]
GSM866858
[25]
GSM866859
[26]
GSM866860
[27]
GSM866861
[28]
GSM866862
[29]
GSM866863
[30]
GSM866864
[31]
GSM866865
[32]
GSM866866
[33]
GSM866867
[34]
GSM866868
[35]
GSM866869
[36]
GSM866870
[37]
GSM866871
[38]
GSM866872
[39]
GSM866873
[40]
GSM866874
[41]
GSM866875
[42]
GSM866876
[43]
GSM866877
[44]
GSM866878
[45]
GSM866879
[46]
GSM866880
[47]
GSM866881
[48]
GSM866882
[49]
GSM866883
[50]
GSM866884
[51]
GSM866885
[52]
GSM866886
[53]
GSM866887
[54]
GSM866888
[55]
GSM866889
[56]
GSM866890
[57]
GSM866891
[58]
GSM866892
[59]
GSM866893
[60]
GSM866894
[61]
GSM866895
[62]
GSM866896
[63]
GSM866897
[64]
GSM866898
[65]
GSM866899
[66]
GSM866900
[67]
GSM866901
[68]
GSM866902
[69]
GSM866903
[70]
GSM866904
[71]
GSM866905
[72]
GSM866906
[73]
GSM866907
[74]
GSM866908
[75]
GSM866909
[76]
GSM866910
[77]
GSM866911
sample_count
78
group_sizes
null
group_sizes_basis
null
platform
1261
taxon
Mus musculus
title
Global developmental gene expression and pathway analysis of normal brain development and mouse models of human neuronal migration defects
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE9566
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=GSE9566
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE9566
version
null
note
Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).
access_statement_kind
repository_route_statement
sample_accessions array · 48 items
[0]
GSM241889
[1]
GSM241890
[2]
GSM241891
[3]
GSM241892
[4]
GSM241893
[5]
GSM241894
[6]
GSM241895
[7]
GSM241896
[8]
GSM241897
[9]
GSM241898
[10]
GSM241899
[11]
GSM241900
[12]
GSM241901
[13]
GSM241902
[14]
GSM241903
[15]
GSM241904
[16]
GSM241905
[17]
GSM241906
[18]
GSM241907
[19]
GSM241908
[20]
GSM241909
[21]
GSM241910
[22]
GSM241911
[23]
GSM241912
[24]
GSM241913
[25]
GSM241914
[26]
GSM241915
[27]
GSM241916
[28]
GSM241917
[29]
GSM241918
[30]
GSM241919
[31]
GSM241920
[32]
GSM241921
[33]
GSM241922
[34]
GSM241923
[35]
GSM241924
[36]
GSM241925
[37]
GSM241926
[38]
GSM241928
[39]
GSM241929
[40]
GSM241930
[41]
GSM241931
[42]
GSM241932
[43]
GSM241933
[44]
GSM241934
[45]
GSM241935
[46]
GSM241936
[47]
GSM241937
sample_count
48
group_sizes
null
group_sizes_basis
null
platform
1261;6096
taxon
Mus musculus
title
A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 16 fields
id
asset:table:pmid:31485792:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:30d2b37965a5fa1aef0e6bfd51baaa6cf9abdcce1d522300f090543f9393266c
bytes
732
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[2]/table-wrap[1]#Tab1
version
null
note
Spatial expression of the NDRGs during development in several species
structure object · 5 fields
pmcid
PMC6754360
section_index
2
section_title
Expression during development
row_count
17
column_count
3
table object · 8 fields
label
Table 1
caption
Spatial expression of the NDRGs during development in several species
rows array · 17 items
[0] array · 3 items
[0]
Gene name
[1]
Species
[2]
Expression area
[1] array · 3 items
[0]
NDRG1
[1]
Xenopus tropicalis [1]
[2]
Forebrain
[2] array · 2 items
[0]
Rat [19]
[1]
Hippocampus
[3] array · 1 item
[0]
Caudate-putamen
[4] array · 3 items
[0]
NDRG2
[1]
Xenopus tropicalis [1]
[2]
Brain
[5] array · 1 item
[0]
Spinal cord
[6] array · 2 items
[0]
Mouse [12, 13]
[1]
Ventricular zone cerebrumSpinal cordChoroid Plexus
[7] array · 3 items
[0]
NDRG3
[1]
Xenopus tropicalis [1]
[2]
Brain
[8] array · 1 item
[0]
Spinal cord
[9] array · 2 items
[0]
Mouse [12]
[1]
Cerebral cortex
[10] array · 1 item
[0]
Spinal Cord
[11] array · 3 items
[0]
NDRG4
[1]
Xenopus tropicalis [1]
[2]
Brain
[12] array · 1 item
[0]
Spinal cord
[13] array · 2 items
[0]
Zebrafish [20]
[1]
Cranial ganglia
[14] array · 1 item
[0]
Hindbrain
[15] array · 1 item
[0]
Tegmentum
[16] array · 1 item
[0]
Cerebellum
locator
section[2]/table-wrap[1]#Tab1
gaps array · 4 items
[0]
asset:data:geo:GSE35366 not downloaded
[1]
asset:data:geo:GSE35366 licence not read
[2]
asset:data:geo:GSE9566 not downloaded
[3]
asset:data:geo:GSE9566 licence not read
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
operations
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
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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 · 2 items
[0]
GSE9566
[1]
GSE35366
resolved_accessions array · 2 items
[0]
GSE9566
[1]
GSE35366
statements array · 1 item
[0]
Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).
basis
The paper names GSE9566, GSE35366 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
[0]
source:pmid:31485792
[1]
data:geo:GSE35366
[2]
asset:table:pmid:31485792:1
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:GSE35366
gaps array · 1 item
[0]
method:not_determinable
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
2026-10-31T18:16:01Z
independence
single_reader
evidence_check object · 2 fields
method
null
availability
null
calls
3
usage object · 3 fields
prompt_tokens
56865
completion_tokens
1470
cached_tokens
648
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:31485792
type
paper
label
pmid:31485792
[1] object · 3 fields
id
source:pmid:31485792
type
manuscript
label
PMID 31485792 full text
[2] object · 3 fields
id
data:geo:GSE35366
type
dataset
label
GEO GSE35366
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:31485792
type
paper
label
pmid:31485792
[1] object · 3 fields
id
source:pmid:31485792
type
manuscript
label
PMID 31485792 full text
[2] object · 3 fields
id
data:geo:GSE35366
type
dataset
label
GEO GSE35366
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-31485792
type
extraction
used array · 1 item
[0]
source:pmid:31485792
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE35366
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE35366
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:31485792
parent_hash
sha256:d5f98d104d6e721a4837a4222a253ac566e4c2d54b1a81316b67f6d1af4350c7
fork_of
null
gaps array · 10 items
[0]
asset:data:geo:GSE35366 licence not read
[1]
asset:data:geo:GSE35366 not downloaded
[2]
asset:data:geo:GSE9566 licence not read
[3]
asset:data:geo:GSE9566 not downloaded
[4]
execution.not_run
[5]
method
[6]
operations
[7]
review.human_critique
[8]
review.independent_reader
[9]
review.machine_critique
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31485792", "kind": "science-record", "revision": 4, "content_hash": "sha256:791b02eab42ce259b5ff78be5f83313bbcc7174994808a78f00ae5f99e5d29e4", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T18:51:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Nervous NDRGs: the N-myc downstream-regulated gene family in the central and peripheral nervous system.", "doi": "10.1007/s10048-019-00587-0", "pmid": "31485792", "authors": ["Simone L Schonkeren", "Maartje Massen", "Raisa van der Horst", "Alexander Koch", "Nathalie Vaes", "Veerle Melotte"], "journal": "Neurogenetics", "year": 2019, "abstract": "The N-Myc downstream-regulated gene (NDRG) family consists of four members (NDRG1, NDRG2, NDRG3, NDRG4) that are differentially expressed in various organs and function in important processes, like cell proliferation and differentiation. In the last couple of decades, interest in this family has risen due to its connection with several disorders of the nervous system including Charcot-Marie-Tooth disease and dementia, as well as nervous system cancers. By combining a literature review with in silico data analysis of publicly available datasets, such as the Mouse Brain Atlas, BrainSpan, the Genotype-Tissue Expression (GTEx) project, and Gene Expression Omnibus (GEO) datasets, this review summarizes the expression and functions of the NDRG family in the healthy and diseased nervous system. We here show that the NDRGs have a differential, relatively cell type-specific, expression pattern in the nervous system. Even though NDRGs share functionalities, like a role in vesicle trafficking, stress response, and neurite outgrowth, other functionalities seem to be unique to a specific member, e.g., the role of NDRG1 in myelination. Furthermore, mutations, phosphorylation, or changes in expression of NDRGs are related to nervous system diseases, including peripheral neuropathy and different forms of dementia. Moreover, NDRG1, NDRG2, and NDRG4 are all involved in cancers of the nervous system, such as glioma, neuroblastoma, or meningioma. All in all, our review elucidates that although the NDRGs belong to the same gene family and share some functional features, they should be considered unique in their expression patterns and functional importance for nervous system development and neuronal diseases.", "claims": [{"id": "claim-data-access", "statement": "Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31485792", "locator": "sections[3] \"Cellular expression\" paragraph 3", "quote": "Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:31485792"], "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:GSE35366"], "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:GSE35366"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31485792", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10048-019-00587-0", "sha256": "sha256:dd14a11fd7ea2c4aaad42476f949d49cff8783a860f8e49f7fa40e5f1707c8c3", "bytes": 69450, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10048-019-00587-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6754360", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE35366", "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=GSE35366", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35366", "version": null, "note": "Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM866834", "GSM866835", "GSM866836", "GSM866837", "GSM866838", "GSM866839", "GSM866840", "GSM866841", "GSM866842", "GSM866843", "GSM866844", "GSM866845", "GSM866846", "GSM866847", "GSM866848", "GSM866849", "GSM866850", "GSM866851", "GSM866852", "GSM866853", "GSM866854", "GSM866855", "GSM866856", "GSM866857", "GSM866858", "GSM866859", "GSM866860", "GSM866861", "GSM866862", "GSM866863", "GSM866864", "GSM866865", "GSM866866", "GSM866867", "GSM866868", "GSM866869", "GSM866870", "GSM866871", "GSM866872", "GSM866873", "GSM866874", "GSM866875", "GSM866876", "GSM866877", "GSM866878", "GSM866879", "GSM866880", "GSM866881", "GSM866882", "GSM866883", "GSM866884", "GSM866885", "GSM866886", "GSM866887", "GSM866888", "GSM866889", "GSM866890", "GSM866891", "GSM866892", "GSM866893", "GSM866894", "GSM866895", "GSM866896", "GSM866897", "GSM866898", "GSM866899", "GSM866900", "GSM866901", "GSM866902", "GSM866903", "GSM866904", "GSM866905", "GSM866906", "GSM866907", "GSM866908", "GSM866909", "GSM866910", "GSM866911"], "sample_count": 78, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Global developmental gene expression and pathway analysis of normal brain development and mouse models of human neuronal migration defects", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE9566", "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=GSE9566", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE9566", "version": null, "note": "Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM241889", "GSM241890", "GSM241891", "GSM241892", "GSM241893", "GSM241894", "GSM241895", "GSM241896", "GSM241897", "GSM241898", "GSM241899", "GSM241900", "GSM241901", "GSM241902", "GSM241903", "GSM241904", "GSM241905", "GSM241906", "GSM241907", "GSM241908", "GSM241909", "GSM241910", "GSM241911", "GSM241912", "GSM241913", "GSM241914", "GSM241915", "GSM241916", "GSM241917", "GSM241918", "GSM241919", "GSM241920", "GSM241921", "GSM241922", "GSM241923", "GSM241924", "GSM241925", "GSM241926", "GSM241928", "GSM241929", "GSM241930", "GSM241931", "GSM241932", "GSM241933", "GSM241934", "GSM241935", "GSM241936", "GSM241937"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "1261;6096", "taxon": "Mus musculus", "title": "A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31485792:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:30d2b37965a5fa1aef0e6bfd51baaa6cf9abdcce1d522300f090543f9393266c", "bytes": 732, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#Tab1", "version": null, "note": "Spatial expression of the NDRGs during development in several species", "structure": {"pmcid": "PMC6754360", "section_index": 2, "section_title": "Expression during development", "row_count": 17, "column_count": 3}, "table": {"label": "Table 1", "caption": "Spatial expression of the NDRGs during development in several species", "rows": [["Gene name", "Species", "Expression area"], ["NDRG1", "Xenopus tropicalis [1]", "Forebrain"], ["Rat [19]", "Hippocampus"], ["Caudate-putamen"], ["NDRG2", "Xenopus tropicalis [1]", "Brain"], ["Spinal cord"], ["Mouse [12, 13]", "Ventricular zone cerebrumSpinal cordChoroid Plexus"], ["NDRG3", "Xenopus tropicalis [1]", "Brain"], ["Spinal cord"], ["Mouse [12]", "Cerebral cortex"], ["Spinal Cord"], ["NDRG4", "Xenopus tropicalis [1]", "Brain"], ["Spinal cord"], ["Zebrafish [20]", "Cranial ganglia"], ["Hindbrain"], ["Tegmentum"], ["Cerebellum"]], "row_count": 17, "column_count": 3, "numeric_cells": 8, "header_rows": 1, "locator": "section[2]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:GSE35366 not downloaded", "asset:data:geo:GSE35366 licence not read", "asset:data:geo:GSE9566 not downloaded", "asset:data:geo:GSE9566 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE9566", "GSE35366"], "resolved_accessions": ["GSE9566", "GSE35366"], "statements": ["Affymetrix GeneChip array expression analysis of the NDRG family members per cell type. Expression values are normalized using MAS5.0, data obtained from GEO (GSE9566)."], "basis": "The paper names GSE9566, GSE35366 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31485792", "data:geo:GSE35366", "asset:table:pmid:31485792:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE35366"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:16:01Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 3, "usage": {"prompt_tokens": 56865, "completion_tokens": 1470, "cached_tokens": 648}}, "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:31485792", "type": "paper", "label": "pmid:31485792"}, {"id": "source:pmid:31485792", "type": "manuscript", "label": "PMID 31485792 full text"}, {"id": "data:geo:GSE35366", "type": "dataset", "label": "GEO GSE35366"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31485792", "type": "paper", "label": "pmid:31485792"}, {"id": "source:pmid:31485792", "type": "manuscript", "label": "PMID 31485792 full text"}, {"id": "data:geo:GSE35366", "type": "dataset", "label": "GEO GSE35366"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31485792", "type": "extraction", "used": ["source:pmid:31485792"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE35366", "type": "accession_resolution", "used": ["data:geo:GSE35366"], "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:31485792", "parent_hash": "sha256:d5f98d104d6e721a4837a4222a253ac566e4c2d54b1a81316b67f6d1af4350c7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE35366 licence not read", "asset:data:geo:GSE35366 not downloaded", "asset:data:geo:GSE9566 licence not read", "asset:data:geo:GSE9566 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"]}