← All .science files
pmid:37261105
Investigation of Underlying Biological Association and Targets between Rejection of Renal Transplant and Renal Cancer.
Yinwei Chen · Zhanpeng Liu · Qian Yu · Xu Sun · Shuai Wang · Qingyi Zhu · Jian Yang · Rongjiang Jiang
International journal of genomics · 2023 doi:10.1155/2023/5542233
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
paper object · 10 fields
authors array · 8 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
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
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 411 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 306 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 1208 items
gaps array · 6 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 3 items
resolved_accessions array · 3 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 2 items
steps array · 1 item
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
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 10 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37261105", "kind": "science-record", "revision": 4, "content_hash": "sha256:bb5c7a00023921afb7ebf4236a40fdd79a96e3cacc7bd59ed90bd85b04232907", "created_at": "2026-11-01T19:01:58Z", "updated_at": "2026-11-01T22:52:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of Underlying Biological Association and Targets between Rejection of Renal Transplant and Renal Cancer.", "doi": "10.1155/2023/5542233", "pmid": "37261105", "authors": ["Yinwei Chen", "Zhanpeng Liu", "Qian Yu", "Xu Sun", "Shuai Wang", "Qingyi Zhu", "Jian Yang", "Rongjiang Jiang"], "journal": "International journal of genomics", "year": 2023, "abstract": "Background: Post-renal transplant patients have a high likelihood of developing renal cancer. However, the underlying biological mechanisms behind the development of renal cancer in post-kidney transplant patients remain to be elucidated. Therefore, this study aimed to investigate the underlying biological mechanism behind the development of renal cell carcinoma in post-renal transplant patients.\nMethods: Next-generation sequencing data and corresponding clinical information of patients with clear cell renal cell carcinoma (ccRCC) were obtained from The Cancer Genome Atlas Program (TCGA) database. The microarray data of kidney transplant patients with or without rejection response was obtained from the Gene Expression Omnibus (GEO) database. In addition, statistical analysis was conducted in R software.\nResults: We identified 55 upregulated genes in the transplant patients with rejection from the GEO datasets (GSE48581, GSE36059, and GSE98320). Furthermore, we conducted bioinformatics analyses, which showed that all of these genes were upregulated in ccRCC tissue. Moreover, a prognosis model was constructed based on four rejection-related genes, including PLAC8, CSTA, AIM2, and LYZ. The prognosis model showed excellent performance in prognosis prediction in a ccRCC cohort. In addition, the machine learning algorithms identified 19 rejection-related genes, including PLAC8, involved in ccRCC occurrence. Finally, the PLAC8 was selected for further research, including its clinical and biological role.\nConclusion: In all, our study provides novel insight into the transition from the rejection of renal transplant to renal cancer. Meanwhile, PLAC8 could be a potential biomarker for ccRCC diagnosis and prognosis in post-kidney transplant patients.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) analysis was utilized to identify the genes differentially expressed in two specific groups using the limma package under the set threshold value (|log2 FC| > 1 and P < 0.05) [16].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37261105", "locator": "sections[4] \"2.2. Differentially Expressed Genes Analysis\" paragraph 2", "quote": "Differentially expressed genes (DEGs) analysis was utilized to identify the genes differentially expressed in two specific groups using the limma package under the set threshold value (|log2 FC| > 1 and P < 0.05) [16]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37261105", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 55 upregulated genes in the transplant patients with rejection from the GEO datasets (GSE48581, GSE36059, and GSE98320).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37261105", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 55 upregulated genes in the transplant patients with rejection from the GEO datasets (GSE48581, GSE36059, and GSE98320)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 55 upregulated genes in the transplant patients with rejection from the GEO datasets (GSE48581, GSE36059, and GSE98320).", "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:37261105"], "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:GSE36059"], "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:GSE36059"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37261105", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2023/5542233", "sha256": "sha256:27b3fed4d693a92b7c9c11471cab976de6db4353ed514318dd8078dcab0de8e6", "bytes": 35964, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2023/5542233", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10229252", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE36059", "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=GSE36059", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36059", "version": null, "note": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM880204", "GSM880205", "GSM880206", "GSM880207", "GSM880208", "GSM880209", "GSM880210", "GSM880211", "GSM880212", "GSM880213", "GSM880214", "GSM880215", "GSM880216", "GSM880217", "GSM880218", "GSM880219", "GSM880220", "GSM880221", "GSM880222", "GSM880223", "GSM880224", "GSM880225", "GSM880226", "GSM880227", "GSM880228", "GSM880229", "GSM880230", "GSM880231", "GSM880232", "GSM880233", "GSM880234", "GSM880235", "GSM880236", "GSM880237", "GSM880238", "GSM880239", "GSM880240", "GSM880241", "GSM880242", "GSM880243", "GSM880244", "GSM880245", "GSM880246", "GSM880247", "GSM880248", "GSM880249", "GSM880250", "GSM880251", "GSM880252", "GSM880253", "GSM880254", "GSM880255", "GSM880256", "GSM880257", "GSM880258", "GSM880259", "GSM880260", "GSM880261", "GSM880262", "GSM880263", "GSM880264", "GSM880265", "GSM880266", "GSM880267", "GSM880268", "GSM880269", "GSM880270", "GSM880271", "GSM880272", "GSM880273", "GSM880274", "GSM880275", "GSM880276", "GSM880277", "GSM880278", "GSM880279", "GSM880280", "GSM880281", "GSM880282", "GSM880283", "GSM880284", "GSM880285", "GSM880286", "GSM880287", "GSM880288", "GSM880289", "GSM880290", "GSM880291", "GSM880292", "GSM880293", "GSM880294", "GSM880295", "GSM880296", "GSM880297", "GSM880298", "GSM880299", "GSM880300", "GSM880301", "GSM880302", "GSM880303", "GSM880304", "GSM880305", "GSM880306", "GSM880307", "GSM880308", "GSM880309", "GSM880310", "GSM880311", "GSM880312", "GSM880313", "GSM880314", "GSM880315", "GSM880316", "GSM880317", "GSM880318", "GSM880319", "GSM880320", "GSM880321", "GSM880322", "GSM880323", "GSM880324", "GSM880325", "GSM880326", "GSM880327", "GSM880328", "GSM880329", "GSM880330", "GSM880331", "GSM880332", "GSM880333", "GSM880334", "GSM880335", "GSM880336", "GSM880337", "GSM880338", "GSM880339", "GSM880340", "GSM880341", "GSM880342", "GSM880343", "GSM880344", "GSM880345", "GSM880346", "GSM880347", "GSM880348", "GSM880349", "GSM880350", "GSM880351", "GSM880352", "GSM880353", "GSM880354", "GSM880355", "GSM880356", "GSM880357", "GSM880358", "GSM880359", "GSM880360", "GSM880361", "GSM880362", "GSM880363", "GSM880364", "GSM880365", "GSM880366", "GSM880367", "GSM880368", "GSM880369", "GSM880370", "GSM880371", "GSM880372", "GSM880373", "GSM880374", "GSM880375", "GSM880376", "GSM880377", "GSM880378", "GSM880379", "GSM880380", "GSM880381", "GSM880382", "GSM880383", "GSM880384", "GSM880385", "GSM880386", "GSM880387", "GSM880388", "GSM880389", "GSM880390", "GSM880391", "GSM880392", "GSM880393", "GSM880394", "GSM880395", "GSM880396", "GSM880397", "GSM880398", "GSM880399", "GSM880400", "GSM880401", "GSM880402", "GSM880403", "GSM880404", "GSM880405", "GSM880406", "GSM880407", "GSM880408", "GSM880409", "GSM880410", "GSM880411", "GSM880412", "GSM880413", "GSM880414", "GSM880415", "GSM880416", "GSM880417", "GSM880418", "GSM880419", "GSM880420", "GSM880421", "GSM880422", "GSM880423", "GSM880424", "GSM880425", "GSM880426", "GSM880427", "GSM880428", "GSM880429", "GSM880430", "GSM880431", "GSM880432", "GSM880433", "GSM880434", "GSM880435", "GSM880436", "GSM880437", "GSM880438", "GSM880439", "GSM880440", "GSM880441", "GSM880442", "GSM880443", "GSM880444", "GSM880445", "GSM880446", "GSM880447", "GSM880448", "GSM880449", "GSM880450", "GSM880451", "GSM880452", "GSM880453", "GSM880454", "GSM880455", "GSM880456", "GSM880457", "GSM880458", "GSM880459", "GSM880460", "GSM880461", "GSM880462", "GSM880463", "GSM880464", "GSM880465", "GSM880466", "GSM880467", "GSM880468", "GSM880469", "GSM880470", "GSM880471", "GSM880472", "GSM880473", "GSM880474", "GSM880475", "GSM880476", "GSM880477", "GSM880478", "GSM880479", "GSM880480", "GSM880481", "GSM880482", "GSM880483", "GSM880484", "GSM880485", "GSM880486", "GSM880487", "GSM880488", "GSM880489", "GSM880490", "GSM880491", "GSM880492", "GSM880493", "GSM880494", "GSM880495", "GSM880496", "GSM880497", "GSM880498", "GSM880499", "GSM880500", "GSM880501", "GSM880502", "GSM880503", "GSM880504", "GSM880505", "GSM880506", "GSM880507", "GSM880508", "GSM880509", "GSM880510", "GSM880511", "GSM880512", "GSM880513", "GSM880514", "GSM880515", "GSM880516", "GSM880517", "GSM880518", "GSM880519", "GSM880520", "GSM880521", "GSM880522", "GSM880523", "GSM880524", "GSM880525", "GSM880526", "GSM880527", "GSM880528", "GSM880529", "GSM880530", "GSM880531", "GSM880532", "GSM880533", "GSM880534", "GSM880535", "GSM880536", "GSM880537", "GSM880538", "GSM880539", "GSM880540", "GSM880541", "GSM880542", "GSM880543", "GSM880544", "GSM880545", "GSM880546", "GSM880547", "GSM880548", "GSM880549", "GSM880550", "GSM880551", "GSM880552", "GSM880553", "GSM880554", "GSM880555", "GSM880556", "GSM880557", "GSM880558", "GSM880559", "GSM880560", "GSM880561", "GSM880562", "GSM880563", "GSM880564", "GSM880565", "GSM880566", "GSM880567", "GSM880568", "GSM880569", "GSM880570", "GSM880571", "GSM880572", "GSM880573", "GSM880574", "GSM880575", "GSM880576", "GSM880577", "GSM880578", "GSM880579", "GSM880580", "GSM880581", "GSM880582", "GSM880583", "GSM880584", "GSM880585", "GSM880586", "GSM880587", "GSM880588", "GSM880589", "GSM880590", "GSM880591", "GSM880592", "GSM880593", "GSM880594", "GSM880595", "GSM880596", "GSM880597", "GSM880598", "GSM880599", "GSM880600", "GSM880601", "GSM880602", "GSM880603", "GSM880604", "GSM880605", "GSM880606", "GSM880607", "GSM880608", "GSM880609", "GSM880610", "GSM880611", "GSM880612", "GSM880613", "GSM880614"], "sample_count": 411, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular diagnosis of T cell-mediated rejection in human kidney transplant biopsies; Molecular diagnosis of antibody-mediated rejection in human kidney transplants", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE48581", "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=GSE48581", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48581", "version": null, "note": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1181496", "GSM1181497", "GSM1181498", "GSM1181499", "GSM1181500", "GSM1181501", "GSM1181502", "GSM1181503", "GSM1181504", "GSM1181505", "GSM1181506", "GSM1181507", "GSM1181508", "GSM1181509", "GSM1181510", "GSM1181511", "GSM1181512", "GSM1181513", "GSM1181514", "GSM1181515", "GSM1181516", "GSM1181517", "GSM1181518", "GSM1181519", "GSM1181520", "GSM1181521", "GSM1181522", "GSM1181523", "GSM1181524", "GSM1181525", "GSM1181526", "GSM1181527", "GSM1181528", "GSM1181529", "GSM1181530", "GSM1181531", "GSM1181532", "GSM1181533", "GSM1181534", "GSM1181535", "GSM1181536", "GSM1181537", "GSM1181538", "GSM1181539", "GSM1181540", "GSM1181541", "GSM1181542", "GSM1181543", "GSM1181544", "GSM1181545", "GSM1181546", "GSM1181547", "GSM1181548", "GSM1181549", "GSM1181550", "GSM1181551", "GSM1181552", "GSM1181553", "GSM1181554", "GSM1181555", "GSM1181556", "GSM1181557", "GSM1181558", "GSM1181559", "GSM1181560", "GSM1181561", "GSM1181562", "GSM1181563", "GSM1181564", "GSM1181565", "GSM1181566", "GSM1181567", "GSM1181568", "GSM1181569", "GSM1181570", "GSM1181571", "GSM1181572", "GSM1181573", "GSM1181574", "GSM1181575", "GSM1181576", "GSM1181577", "GSM1181578", "GSM1181580", "GSM1181582", "GSM1181584", "GSM1181586", "GSM1181588", "GSM1181590", "GSM1181591", "GSM1181592", "GSM1181593", "GSM1181594", "GSM1181595", "GSM1181596", "GSM1181597", "GSM1181598", "GSM1181599", "GSM1181600", "GSM1181601", "GSM1181602", "GSM1181603", "GSM1181604", "GSM1181605", "GSM1181606", "GSM1181607", "GSM1181608", "GSM1181609", "GSM1181610", "GSM1181611", "GSM1181612", "GSM1181613", "GSM1181614", "GSM1181615", "GSM1181616", "GSM1181617", "GSM1181618", "GSM1181619", "GSM1181620", "GSM1181621", "GSM1181622", "GSM1181623", "GSM1181624", "GSM1181625", "GSM1181626", "GSM1181627", "GSM1181628", "GSM1181629", "GSM1181630", "GSM1181631", "GSM1181632", "GSM1181633", "GSM1181634", "GSM1181635", "GSM1181636", "GSM1181637", "GSM1181638", "GSM1181639", "GSM1181640", "GSM1181641", "GSM1181643", "GSM1181644", "GSM1181645", "GSM1181648", "GSM1181651", "GSM1181653", "GSM1181654", "GSM1181656", "GSM1181658", "GSM1181660", "GSM1181661", "GSM1181662", "GSM1181663", "GSM1181664", "GSM1181665", "GSM1181666", "GSM1181667", "GSM1181668", "GSM1181669", "GSM1181670", "GSM1181671", "GSM1181672", "GSM1181673", "GSM1181674", "GSM1181675", "GSM1181676", "GSM1181677", "GSM1181678", "GSM1181679", "GSM1181680", "GSM1181681", "GSM1181682", "GSM1181683", "GSM1181684", "GSM1181685", "GSM1181686", "GSM1181687", "GSM1181688", "GSM1181689", "GSM1181690", "GSM1181691", "GSM1181692", "GSM1181693", "GSM1181694", "GSM1181695", "GSM1181696", "GSM1181697", "GSM1181698", "GSM1181699", "GSM1181700", "GSM1181701", "GSM1181702", "GSM1181703", "GSM1181704", "GSM1181705", "GSM1181706", "GSM1181707", "GSM1181708", "GSM1181709", "GSM1181710", "GSM1181711", "GSM1181712", "GSM1181713", "GSM1181714", "GSM1181715", "GSM1181716", "GSM1181717", "GSM1181718", "GSM1181719", "GSM1181720", "GSM1181721", "GSM1181722", "GSM1181723", "GSM1181724", "GSM1181725", "GSM1181726", "GSM1181727", "GSM1181728", "GSM1181729", "GSM1181730", "GSM1181731", "GSM1181732", "GSM1181733", "GSM1181734", "GSM1181735", "GSM1181736", "GSM1181737", "GSM1181738", "GSM1181739", "GSM1181740", "GSM1181741", "GSM1181742", "GSM1181743", "GSM1181744", "GSM1181745", "GSM1181746", "GSM1181747", "GSM1181748", "GSM1181749", "GSM1181750", "GSM1181751", "GSM1181752", "GSM1181753", "GSM1181754", "GSM1181755", "GSM1181756", "GSM1181757", "GSM1181758", "GSM1181759", "GSM1181760", "GSM1181761", "GSM1181762", "GSM1181763", "GSM1181764", "GSM1181765", "GSM1181766", "GSM1181767", "GSM1181768", "GSM1181769", "GSM1181770", "GSM1181771", "GSM1181772", "GSM1181773", "GSM1181774", "GSM1181775", "GSM1181776", "GSM1181777", "GSM1181778", "GSM1181779", "GSM1181780", "GSM1181781", "GSM1181782", "GSM1181783", "GSM1181784", "GSM1181785", "GSM1181786", "GSM1181787", "GSM1181788", "GSM1181789", "GSM1181790", "GSM1181791", "GSM1181792", "GSM1181793", "GSM1181794", "GSM1181795", "GSM1181796", "GSM1181797", "GSM1181798", "GSM1181799", "GSM1181800", "GSM1181801", "GSM1181802", "GSM1181803", "GSM1181804", "GSM1181805", "GSM1181806", "GSM1181807", "GSM1181808", "GSM1181809", "GSM1181810", "GSM1181811", "GSM1181812", "GSM1181813", "GSM1181814", "GSM1181815", "GSM1181816"], "sample_count": 306, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Potential impact of microarray diagnosis of T cell-mediated rejection in kidney transplants: the INTERCOM study", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE98320", "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=GSE98320", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98320", "version": null, "note": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2590943", "GSM2590944", "GSM2590945", "GSM2590946", "GSM2590947", "GSM2590948", "GSM2590949", "GSM2590950", "GSM2590951", "GSM2590952", "GSM2590953", "GSM2590954", "GSM2590955", "GSM2590956", "GSM2590957", "GSM2590958", "GSM2590959", "GSM2590960", "GSM2590961", "GSM2590962", "GSM2590963", "GSM2590964", "GSM2590965", "GSM2590966", "GSM2590967", "GSM2590968", "GSM2590969", "GSM2590970", "GSM2590971", "GSM2590972", "GSM2590973", "GSM2590974", "GSM2590975", "GSM2590976", "GSM2590977", "GSM2590978", "GSM2590979", "GSM2590980", "GSM2590981", "GSM2590982", "GSM2590983", "GSM2590984", "GSM2590985", "GSM2590986", "GSM2590987", "GSM2590988", "GSM2590989", "GSM2590990", "GSM2590991", "GSM2590992", "GSM2590993", "GSM2590994", "GSM2590995", "GSM2590996", "GSM2590997", "GSM2590998", "GSM2590999", "GSM2591000", "GSM2591001", "GSM2591002", "GSM2591003", "GSM2591004", "GSM2591005", "GSM2591006", "GSM2591007", "GSM2591008", "GSM2591009", "GSM2591010", "GSM2591011", "GSM2591012", "GSM2591013", "GSM2591014", "GSM2591015", "GSM2591016", "GSM2591017", "GSM2591018", "GSM2591019", "GSM2591020", "GSM2591021", "GSM2591022", "GSM2591023", "GSM2591024", "GSM2591025", "GSM2591026", "GSM2591027", "GSM2591028", "GSM2591029", "GSM2591030", "GSM2591031", "GSM2591032", "GSM2591033", "GSM2591034", "GSM2591035", "GSM2591036", "GSM2591037", "GSM2591038", "GSM2591039", "GSM2591040", "GSM2591041", "GSM2591042", "GSM2591043", "GSM2591044", "GSM2591045", "GSM2591046", "GSM2591047", "GSM2591048", "GSM2591049", "GSM2591050", "GSM2591051", "GSM2591052", "GSM2591053", "GSM2591054", "GSM2591055", "GSM2591056", "GSM2591057", "GSM2591058", "GSM2591059", "GSM2591060", "GSM2591061", "GSM2591062", "GSM2591063", "GSM2591064", "GSM2591065", "GSM2591066", "GSM2591067", "GSM2591068", "GSM2591069", "GSM2591070", "GSM2591071", "GSM2591072", "GSM2591073", "GSM2591074", "GSM2591075", "GSM2591076", "GSM2591077", "GSM2591078", "GSM2591079", "GSM2591080", "GSM2591081", "GSM2591082", "GSM2591083", "GSM2591084", "GSM2591085", "GSM2591086", "GSM2591087", "GSM2591088", "GSM2591089", "GSM2591090", "GSM2591091", "GSM2591092", "GSM2591093", "GSM2591094", "GSM2591095", "GSM2591096", "GSM2591097", "GSM2591098", "GSM2591099", "GSM2591100", "GSM2591101", "GSM2591102", "GSM2591103", "GSM2591104", "GSM2591105", "GSM2591106", "GSM2591107", "GSM2591108", "GSM2591109", "GSM2591110", "GSM2591111", "GSM2591112", "GSM2591113", "GSM2591114", "GSM2591115", "GSM2591116", "GSM2591117", "GSM2591118", "GSM2591119", "GSM2591120", "GSM2591121", "GSM2591122", "GSM2591123", "GSM2591124", "GSM2591125", "GSM2591126", "GSM2591127", "GSM2591128", "GSM2591129", "GSM2591130", "GSM2591131", "GSM2591132", "GSM2591133", "GSM2591134", "GSM2591135", "GSM2591136", "GSM2591137", "GSM2591138", "GSM2591139", "GSM2591140", "GSM2591141", "GSM2591142", "GSM2591143", "GSM2591144", "GSM2591145", "GSM2591146", "GSM2591147", "GSM2591148", "GSM2591149", "GSM2591150", "GSM2591151", "GSM2591152", "GSM2591153", "GSM2591154", "GSM2591155", "GSM2591156", "GSM2591157", "GSM2591158", "GSM2591159", "GSM2591160", "GSM2591161", "GSM2591162", "GSM2591163", "GSM2591164", "GSM2591165", "GSM2591166", "GSM2591167", "GSM2591168", "GSM2591169", "GSM2591170", "GSM2591171", "GSM2591172", "GSM2591173", "GSM2591174", "GSM2591175", "GSM2591176", "GSM2591177", "GSM2591178", "GSM2591179", "GSM2591180", "GSM2591181", "GSM2591182", "GSM2591183", "GSM2591184", "GSM2591185", "GSM2591186", "GSM2591187", "GSM2591188", "GSM2591189", "GSM2591190", "GSM2591191", "GSM2591192", "GSM2591193", "GSM2591194", "GSM2591195", "GSM2591196", "GSM2591197", "GSM2591198", "GSM2591199", "GSM2591200", "GSM2591201", "GSM2591202", "GSM2591203", "GSM2591204", "GSM2591205", "GSM2591206", "GSM2591207", "GSM2591208", "GSM2591209", "GSM2591210", "GSM2591211", "GSM2591212", "GSM2591213", "GSM2591214", "GSM2591215", "GSM2591216", "GSM2591217", "GSM2591218", "GSM2591219", "GSM2591220", "GSM2591221", "GSM2591222", "GSM2591223", "GSM2591224", "GSM2591225", "GSM2591226", "GSM2591227", "GSM2591228", "GSM2591229", "GSM2591230", "GSM2591231", "GSM2591232", "GSM2591233", "GSM2591234", "GSM2591235", "GSM2591236", "GSM2591237", "GSM2591238", "GSM2591239", "GSM2591240", "GSM2591241", "GSM2591242", "GSM2591243", "GSM2591244", "GSM2591245", "GSM2591246", "GSM2591247", "GSM2591248", "GSM2591249", "GSM2591250", "GSM2591251", "GSM2591252", "GSM2591253", "GSM2591254", "GSM2591255", "GSM2591256", "GSM2591257", "GSM2591258", "GSM2591259", "GSM2591260", "GSM2591261", "GSM2591262", "GSM2591263", "GSM2591264", "GSM2591265", "GSM2591266", "GSM2591267", "GSM2591268", "GSM2591269", "GSM2591270", "GSM2591271", "GSM2591272", "GSM2591273", "GSM2591274", "GSM2591275", "GSM2591276", "GSM2591277", "GSM2591278", "GSM2591279", "GSM2591280", "GSM2591281", "GSM2591282", "GSM2591283", "GSM2591284", "GSM2591285", "GSM2591286", "GSM2591287", "GSM2591288", "GSM2591289", "GSM2591290", "GSM2591291", "GSM2591292", "GSM2591293", "GSM2591294", "GSM2591295", "GSM2591296", "GSM2591297", "GSM2591298", "GSM2591299", "GSM2591300", "GSM2591301", "GSM2591302", "GSM2591303", "GSM2591304", "GSM2591305", "GSM2591306", "GSM2591307", "GSM2591308", "GSM2591309", "GSM2591310", "GSM2591311", "GSM2591312", "GSM2591313", "GSM2591314", "GSM2591315", "GSM2591316", "GSM2591317", "GSM2591318", "GSM2591319", "GSM2591320", "GSM2591321", "GSM2591322", "GSM2591323", "GSM2591324", "GSM2591325", "GSM2591326", "GSM2591327", "GSM2591328", "GSM2591329", "GSM2591330", "GSM2591331", "GSM2591332", "GSM2591333", "GSM2591334", "GSM2591335", "GSM2591336", "GSM2591337", "GSM2591338", "GSM2591339", "GSM2591340", "GSM2591341", "GSM2591342", "GSM2591343", "GSM2591344", "GSM2591345", "GSM2591346", "GSM2591347", "GSM2591348", "GSM2591349", "GSM2591350", "GSM2591351", "GSM2591352", "GSM2591353", "GSM2591354", "GSM2591355", "GSM2591356", "GSM2591357", "GSM2591358", "GSM2591359", "GSM2591360", "GSM2591361", "GSM2591362", "GSM2591363", "GSM2591364", "GSM2591365", "GSM2591366", "GSM2591367", "GSM2591368", "GSM2591369", "GSM2591370", "GSM2591371", "GSM2591372", "GSM2591373", "GSM2591374", "GSM2591375", "GSM2591376", "GSM2591377", "GSM2591378", "GSM2591379", "GSM2591380", "GSM2591381", "GSM2591382", "GSM2591383", "GSM2591384", "GSM2591385", "GSM2591386", "GSM2591387", "GSM2591388", "GSM2591389", "GSM2591390", "GSM2591391", "GSM2591392", "GSM2591393", "GSM2591394", "GSM2591395", "GSM2591396", "GSM2591397", "GSM2591398", "GSM2591399", "GSM2591400", "GSM2591401", "GSM2591402", "GSM2591403", "GSM2591404", "GSM2591405", "GSM2591406", "GSM2591407", "GSM2591408", "GSM2591409", "GSM2591410", "GSM2591411", "GSM2591412", "GSM2591413", "GSM2591414", "GSM2591415", "GSM2591416", "GSM2591417", "GSM2591418", "GSM2591419", "GSM2591420", "GSM2591421", "GSM2591422", "GSM2591423", "GSM2591424", "GSM2591425", "GSM2591426", "GSM2591427", "GSM2591428", "GSM2591429", "GSM2591430", "GSM2591431", "GSM2591432", "GSM2591433", "GSM2591434", "GSM2591435", "GSM2591436", "GSM2591437", "GSM2591438", "GSM2591439", "GSM2591440", "GSM2591441", "GSM2591442", "GSM2591443", "GSM2591444", "GSM2591445", "GSM2591446", "GSM2591447", "GSM2591448", "GSM2591449", "GSM2591450", "GSM2591451", "GSM2591452", "GSM2591453", "GSM2591454", "GSM2591455", "GSM2591456", "GSM2591457", "GSM2591458", "GSM2591459", "GSM2591460", "GSM2591461", "GSM2591462", "GSM2591463", "GSM2591464", "GSM2591465", "GSM2591466", "GSM2591467", "GSM2591468", "GSM2591469", "GSM2591470", "GSM2591471", "GSM2591472", "GSM2591473", "GSM2591474", "GSM2591475", "GSM2591476", "GSM2591477", "GSM2591478", "GSM2591479", "GSM2591480", "GSM2591481", "GSM2591482", "GSM2591483", "GSM2591484", "GSM2591485", "GSM2591486", "GSM2591487", "GSM2591488", "GSM2591489", "GSM2591490", "GSM2591491", "GSM2591492", "GSM2591493", "GSM2591494", "GSM2591495", "GSM2591496", "GSM2591497", "GSM2591498", "GSM2591499", "GSM2591500", "GSM2591501", "GSM2591502", "GSM2591503", "GSM2591504", "GSM2591505", "GSM2591506", "GSM2591507", "GSM2591508", "GSM2591509", "GSM2591510", "GSM2591511", "GSM2591512", "GSM2591513", "GSM2591514", "GSM2591515", "GSM2591516", "GSM2591517", "GSM2591518", "GSM2591519", "GSM2591520", "GSM2591521", "GSM2591522", "GSM2591523", "GSM2591524", "GSM2591525", "GSM2591526", "GSM2591527", "GSM2591528", "GSM2591529", "GSM2591530", "GSM2591531", "GSM2591532", "GSM2591533", "GSM2591534", "GSM2591535", "GSM2591536", "GSM2591537", "GSM2591538", "GSM2591539", "GSM2591540", "GSM2591541", "GSM2591542", "GSM2591543", "GSM2591544", "GSM2591545", "GSM2591546", "GSM2591547", "GSM2591548", "GSM2591549", "GSM2591550", "GSM2591551", "GSM2591552", "GSM2591553", "GSM2591554", "GSM2591555", "GSM2591556", "GSM2591557", "GSM2591558", "GSM2591559", "GSM2591560", "GSM2591561", "GSM2591562", "GSM2591563", "GSM2591564", "GSM2591565", "GSM2591566", "GSM2591567", "GSM2591568", "GSM2591569", "GSM2591570", "GSM2591571", "GSM2591572", "GSM2591573", "GSM2591574", "GSM2591575", "GSM2591576", "GSM2591577", "GSM2591578", "GSM2591579", "GSM2591580", "GSM2591581", "GSM2591582", "GSM2591583", "GSM2591584", "GSM2591585", "GSM2591586", "GSM2591587", "GSM2591588", "GSM2591589", "GSM2591590", "GSM2591591", "GSM2591592", "GSM2591593", "GSM2591594", "GSM2591595", "GSM2591596", "GSM2591597", "GSM2591598", "GSM2591599", "GSM2591600", "GSM2591601", "GSM2591602", "GSM2591603", "GSM2591604", "GSM2591605", "GSM2591606", "GSM2591607", "GSM2591608", "GSM2591609", "GSM2591610", "GSM2591611", "GSM2591612", "GSM2591613", "GSM2591614", "GSM2591615", "GSM2591616", "GSM2591617", "GSM2591618", "GSM2591619", "GSM2591620", "GSM2591621", "GSM2591622", "GSM2591623", "GSM2591624", "GSM2591625", "GSM2591626", "GSM2591627", "GSM2591628", "GSM2591629", "GSM2591630", "GSM2591631", "GSM2591632", "GSM2591633", "GSM2591634", "GSM2591635", "GSM2591636", "GSM2591637", "GSM2591638", "GSM2591639", "GSM2591640", "GSM2591641", "GSM2591642", "GSM2591643", "GSM2591644", "GSM2591645", "GSM2591646", "GSM2591647", "GSM2591650", "GSM2591652", "GSM2591654", "GSM2591657", "GSM2591658", "GSM2591659", "GSM2591660", "GSM2591661", "GSM2591662", "GSM2591663", "GSM2591664", "GSM2591665", "GSM2591666", "GSM2591667", "GSM2591668", "GSM2591669", "GSM2591670", "GSM2591671", "GSM2591672", "GSM2591673", "GSM2591674", "GSM2591675", "GSM2591676", "GSM2591677", "GSM2591678", "GSM2591679", "GSM2591680", "GSM2591681", "GSM2591682", "GSM2591683", "GSM2591684", "GSM2591685", "GSM2591686", "GSM2591687", "GSM2591688", "GSM2591689", "GSM2591690", "GSM2591691", "GSM2591692", "GSM2591693", "GSM2591694", "GSM2591695", "GSM2591696", "GSM2591697", "GSM2591698", "GSM2591699", "GSM2591700", "GSM2591701", "GSM2591702", "GSM2591703", "GSM2591704", "GSM2591705", "GSM2591706", "GSM2591707", "GSM2591708", "GSM2591709", "GSM2591710", "GSM2591711", "GSM2591712", "GSM2591713", "GSM2591714", "GSM2591715", "GSM2591716", "GSM2591717", "GSM2591718", "GSM2591719", "GSM2591720", "GSM2591721", "GSM2591722", "GSM2591723", "GSM2591724", "GSM2591725", "GSM2591726", "GSM2591727", "GSM2591728", "GSM2591729", "GSM2591730", "GSM2591731", "GSM2591732", "GSM2591733", "GSM2591734", "GSM2591735", "GSM2591736", "GSM2591737", "GSM2591738", "GSM2591739", "GSM2591740", "GSM2591741", "GSM2591742", "GSM2591743", "GSM2591744", "GSM2591745", "GSM2591746", "GSM2591747", "GSM2591748", "GSM2591749", "GSM2591750", "GSM2591751", "GSM2591752", "GSM2591753", "GSM2591754", "GSM2591755", "GSM2591756", "GSM2591757", "GSM2591758", "GSM2591759", "GSM2591760", "GSM2591761", "GSM2591762", "GSM2591763", "GSM2591764", "GSM2591765", "GSM2591766", "GSM2591767", "GSM2591768", "GSM2591769", "GSM2591770", "GSM2591771", "GSM2591772", "GSM2591773", "GSM2591774", "GSM2591775", "GSM2591776", "GSM2591777", "GSM2591778", "GSM2591779", "GSM2591780", "GSM2591781", "GSM2591782", "GSM2591783", "GSM2591784", "GSM2591785", "GSM2591786", "GSM2591787", "GSM2591788", "GSM2591789", "GSM2591790", "GSM2591791", "GSM2591792", "GSM2591793", "GSM2591794", "GSM2591795", "GSM2591796", "GSM2591797", "GSM2591798", "GSM2591799", "GSM2591800", "GSM2591801", "GSM2591802", "GSM2591803", "GSM2591804", "GSM2591805", "GSM2591806", "GSM2591807", "GSM2591808", "GSM2591809", "GSM2591810", "GSM2591811", "GSM2591812", "GSM2591813", "GSM2591814", "GSM2591815", "GSM2591816", "GSM2591817", "GSM2591818", "GSM2591819", "GSM2591820", "GSM2591821", "GSM2591822", "GSM2591823", "GSM2591824", "GSM2591825", "GSM2591826", "GSM2591827", "GSM2591828", "GSM2591829", "GSM2591830", "GSM2591831", "GSM2591832", "GSM2591833", "GSM2591834", "GSM2591835", "GSM2591836", "GSM2591837", "GSM2591838", "GSM2591839", "GSM2591840", "GSM2591841", "GSM2591842", "GSM2591843", "GSM2591844", "GSM2591845", "GSM2591846", "GSM2591847", "GSM2591848", "GSM2591849", "GSM2591850", "GSM2591851", "GSM2591852", "GSM2591853", "GSM2591854", "GSM2591855", "GSM2591856", "GSM2591857", "GSM2591858", "GSM2591859", "GSM2591860", "GSM2591861", "GSM2591862", "GSM2591863", "GSM2591864", "GSM2591865", "GSM2591866", "GSM2591867", "GSM2591868", "GSM2591869", "GSM2591870", "GSM2591871", "GSM2591872", "GSM2591873", "GSM2591874", "GSM2591875", "GSM2591876", "GSM2591877", "GSM2591878", "GSM2591879", "GSM2591880", "GSM2591881", "GSM2591882", "GSM2591883", "GSM2591884", "GSM2591885", "GSM2591886", "GSM2591887", "GSM2591888", "GSM2591889", "GSM2591890", "GSM2591891", "GSM2591892", "GSM2591893", "GSM2591894", "GSM2591895", "GSM2591896", "GSM2591897", "GSM2591898", "GSM2591899", "GSM2591900", "GSM2591901", "GSM2591902", "GSM2591903", "GSM2591904", "GSM2591905", "GSM2591906", "GSM2591907", "GSM2591908", "GSM2591909", "GSM2591910", "GSM2591911", "GSM2591912", "GSM2591913", "GSM2591914", "GSM2591915", "GSM2591916", "GSM2591917", "GSM2591918", "GSM2591919", "GSM2591920", "GSM2591921", "GSM2591922", "GSM2591923", "GSM2591924", "GSM2591925", "GSM2591926", "GSM2591927", "GSM2591928", "GSM2591929", "GSM2591930", "GSM2591931", "GSM2591932", "GSM2591933", "GSM2591934", "GSM2591935", "GSM2591936", "GSM2591937", "GSM2591938", "GSM2591939", "GSM2591940", "GSM2591941", "GSM2591942", "GSM2591943", "GSM2591944", "GSM2591945", "GSM2591946", "GSM2591947", "GSM2591948", "GSM2591949", "GSM2591950", "GSM2591951", "GSM2591952", "GSM2591953", "GSM2591954", "GSM2591955", "GSM2591956", "GSM2591957", "GSM2591958", "GSM2591959", "GSM2591960", "GSM2591961", "GSM2591962", "GSM2591963", "GSM2591964", "GSM2591965", "GSM2591966", "GSM2591967", "GSM2591968", "GSM2591969", "GSM2591970", "GSM2591971", "GSM2591972", "GSM2591973", "GSM2591974", "GSM2591975", "GSM2591976", "GSM2591977", "GSM2591978", "GSM2591979", "GSM2591980", "GSM2591981", "GSM2591982", "GSM2591983", "GSM2591984", "GSM2591985", "GSM2591986", "GSM2591987", "GSM2591988", "GSM2591989", "GSM2591990", "GSM2591991", "GSM2591992", "GSM2591993", "GSM2591994", "GSM2591995", "GSM2591996", "GSM2591997", "GSM2591998", "GSM2591999", "GSM2592000", "GSM2592001", "GSM2592002", "GSM2592003", "GSM2592004", "GSM2592005", "GSM2592006", "GSM2592007", "GSM2592008", "GSM2592009", "GSM2592010", "GSM2592011", "GSM2592012", "GSM2592013", "GSM2592014", "GSM2592015", "GSM2592016", "GSM2592017", "GSM2592018", "GSM2592019", "GSM2592020", "GSM2592021", "GSM2592022", "GSM2592023", "GSM2592024", "GSM2592025", "GSM2592026", "GSM2592027", "GSM2592028", "GSM2592029", "GSM2592030", "GSM2592031", "GSM2592032", "GSM2592033", "GSM2592034", "GSM2592035", "GSM2592036", "GSM2592037", "GSM2592038", "GSM2592039", "GSM2592040", "GSM2592041", "GSM2592042", "GSM2592043", "GSM2592044", "GSM2592045", "GSM2592046", "GSM2592047", "GSM2592048", "GSM2592049", "GSM2592050", "GSM2592051", "GSM2592052", "GSM2592053", "GSM2592054", "GSM2592055", "GSM2592056", "GSM2592057", "GSM2592058", "GSM2592059", "GSM2592060", "GSM2592061", "GSM2592062", "GSM2592063", "GSM2592064", "GSM2592065", "GSM2592066", "GSM2592067", "GSM2592068", "GSM2592069", "GSM2592070", "GSM2592071", "GSM2592072", "GSM2592073", "GSM2592074", "GSM2592075", "GSM2592076", "GSM2592077", "GSM2592078", "GSM2592079", "GSM2592080", "GSM2592081", "GSM2592082", "GSM2592083", "GSM2592084", "GSM2592085", "GSM2592086", "GSM2592087", "GSM2592088", "GSM2592089", "GSM2592090", "GSM2592091", "GSM2592092", "GSM2592093", "GSM2592094", "GSM2592095", "GSM2592096", "GSM2592097", "GSM2592098", "GSM2592099", "GSM2592100", "GSM2592101", "GSM2592102", "GSM2592103", "GSM2592104", "GSM2592105", "GSM2592106", "GSM2592107", "GSM2592108", "GSM2592109", "GSM2592110", "GSM2592111", "GSM2592112", "GSM2592113", "GSM2592114", "GSM2592115", "GSM2592116", "GSM2592117", "GSM2592118", "GSM2592119", "GSM2592120", "GSM2592121", "GSM2592122", "GSM2592123", "GSM2592124", "GSM2592125", "GSM2592126", "GSM2592127", "GSM2592128", "GSM2592129", "GSM2592130", "GSM2592131", "GSM2592132", "GSM2592133", "GSM2592134", "GSM2592135", "GSM2592136", "GSM2592137", "GSM2592138", "GSM2592139", "GSM2592140", "GSM2592141", "GSM2592142", "GSM2592143", "GSM2592144", "GSM2592145", "GSM2592146", "GSM2592147", "GSM2592148", "GSM2592149", "GSM2592150", "GSM2592151", "GSM2592152", "GSM2592153", "GSM2592154", "GSM2592155", "GSM2592156"], "sample_count": 1208, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "Assessing rejection-related disease in kidney transplant biopsies based on archetypal analysis of molecular phenotypes", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE36059 not downloaded", "asset:data:geo:GSE36059 licence not read", "asset:data:geo:GSE48581 not downloaded", "asset:data:geo:GSE48581 licence not read", "asset:data:geo:GSE98320 not downloaded", "asset:data:geo:GSE98320 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes (DEGs) analysis was utilized to identify the genes differentially expressed in two specific groups using the limma package under the set threshold value (|log2 FC| > 1 and P < 0.05) [16]."}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE48581", "GSE36059", "GSE98320"], "resolved_accessions": ["GSE48581", "GSE36059", "GSE98320"], "statements": ["The transcriptional profile data of kidney transplant patients with or without rejection response can be obtained from GSE48581, GSE36059, and GSE98320 in Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Pan-cancer data was obtained from the USCS XENA website (https://xenabrowser.net/)."], "basis": "The paper names GSE48581, GSE36059, GSE98320 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37261105", "data:geo:GSE36059"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE36059"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:42:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11415, "completion_tokens": 1959, "cached_tokens": 256}}, "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:37261105", "type": "paper", "label": "pmid:37261105"}, {"id": "source:pmid:37261105", "type": "manuscript", "label": "PMID 37261105 full text"}, {"id": "data:geo:GSE36059", "type": "dataset", "label": "GEO GSE36059"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37261105", "type": "paper", "label": "pmid:37261105"}, {"id": "source:pmid:37261105", "type": "manuscript", "label": "PMID 37261105 full text"}, {"id": "data:geo:GSE36059", "type": "dataset", "label": "GEO GSE36059"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37261105", "type": "extraction", "used": ["source:pmid:37261105"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE36059", "type": "accession_resolution", "used": ["data:geo:GSE36059"], "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:37261105", "parent_hash": "sha256:ab168b6e237a3522108ec2fec1690d1d51258b8fd23bd50ca785e4b294a1f2a6", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE36059 licence not read", "asset:data:geo:GSE36059 not downloaded", "asset:data:geo:GSE48581 licence not read", "asset:data:geo:GSE48581 not downloaded", "asset:data:geo:GSE98320 licence not read", "asset:data:geo:GSE98320 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["in post-renal transplant patients. Methods: Next-generation sequencing data and corresponding clinical information"], "order_basis": "paper_text_order:484", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["er Genome Atlas Program (TCGA) database. The microarray data of kidney transplant patients with or w"], "order_basis": "paper_text_order:683", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) analysis was utilized to identify the genes differentially expressed in two specific groups using the limma package under the set threshold value (|log2 FC| > 1 and P < 0.05) [16]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}