← All .science files
pmid:32922167
Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics Analysis.
Qin Yang · Kaihu Li · Xin Li · Jing Liu
International journal of medical sciences · 2020 doi:10.7150/ijms.48244
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 4 items
claims array · 2 items
[0] object · 6 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 · 10 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 14 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 559 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 16 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 8 items
[1] array · 8 items
[2] array · 8 items
[3] array · 8 items
[4] array · 8 items
[5] array · 8 items
[6] array · 8 items
[7] array · 8 items
[8] array · 8 items
[9] array · 8 items
[10] array · 8 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 31 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[26] array · 6 items
[27] array · 6 items
[28] array · 6 items
[29] array · 6 items
[30] array · 6 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 16 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[9] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 10 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
gaps array · 4 items
analysis object · 4 fields
methods array · 6 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[4] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[5] 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 · 1 item
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 · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 9 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 · 9 items
assays array · 1 item
[0] 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:32922167", "kind": "science-record", "revision": 9, "content_hash": "sha256:d6588c17d2a8a4c7ec98551970df8e371f6013cd02ce03fb36e7eff14956dd55", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T22:45:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics Analysis.", "doi": "10.7150/ijms.48244", "pmid": "32922167", "authors": ["Qin Yang", "Kaihu Li", "Xin Li", "Jing Liu"], "journal": "International journal of medical sciences", "year": 2020, "abstract": "Background: Multiple myeloma (MM) is the second most common hematological malignancy, which is still incurable and relapses inevitably, highlighting further understanding of the possible mechanisms. Side population (SP) cells are a group of enriched progenitor cells showing stem-like phenotypes with a distinct low-staining pattern with Hoechst 33342. Compared to main population (MP) cells, the underlying molecular characteristics of SP cells remain largely unclear. This bioinformatics analysis aimed to identify key genes and pathways in myeloma SP cells to provide novel biomarkers, predict MM prognosis and advance potential therapeutic targets. Methods: The gene expression profile GSE109651 was obtained from Gene Expression Omnibus database, and then differentially expressed genes (DEGs) with P-value <0.05 and |log2 fold-change (FC)| > 2 were selected by the comparison of myeloma light-chain (LC) restricted SP (LC/SP) cells and MP CD138+ cells. Subsequently, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis, protein-protein interaction (PPI) network analysis were performed to identify the functional enrichment analysis of the DEGs and screen hub genes. Cox proportional hazards regression was used to select the potential prognostic DEGs in training dataset (GSE2658). The prognostic value of the potential prognostic genes was evaluated by Kaplan-Meier curve and validated in another external dataset (MMRF-CoMMpass cohort from TCGA). Results: Altogether, 403 up-regulated and 393 down-regulated DEGs were identified. GO analysis showed that the up-regulated DEGs were significantly enriched in innate immune response, inflammatory response, plasma membrane and integral component of membrane, while the down-regulated DEGs were mainly involved in protoporphyrinogen IX and heme biosynthetic process, hemoglobin complex and erythrocyte differentiation. KEGG pathway analysis suggested that the DEGs were significantly enriched in osteoclast differentiation, porphyrin and chlorophyll metabolism and cytokine-cytokine receptor interaction. The top 10 hub genes, identified by the plug-in cytoHubba of the Cytoscape software using maximal clique centrality (MCC) algorithm, were ITGAM, MMP9, ITGB2, FPR2, C3AR1, CXCL1, CYBB, LILRB2, HP and FCER1G. Modules and corresponding GO enrichment analysis indicated that myeloma LC/SP cells were significantly associated with immune system, immune response and cell cycle. The predictive value of the prognostic model including TFF3, EPDR1, MACROD1, ARHGEF12, AMMECR1, NFATC2, HES6, PLEK2 and SNCA was identified, and validated in another external dataset (MMRF-CoMMpass cohort from TCGA). Conclusions: In conclusion, this study provides reliable molecular biomarkers for screening, prognosis, as well as novel therapeutic targets for myeloma LC/SP cells.", "claims": [{"id": "claim-method", "statement": "Then, DEGs between LC/SP cells and MP CD138+ cells of MM were identified by an empirical Bayes method based on the “limma” package in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32922167", "locator": "sections[4] \"Data processing and identification of DEGs of GSE109651\" paragraph 3", "quote": "Then, DEGs between LC/SP cells and MP CD138+ cells of MM were identified by an empirical Bayes method based on the “limma” package in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138+ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32922167", "locator": "sections[3] \"Microarray data profile\" paragraph 2", "quote": "The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138+ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody."}], "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:32922167"], "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:GSE109651"], "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:GSE109651"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32922167", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/ijms.48244", "sha256": "sha256:5b9991321047c5319e749af90e9ff7aef91133930fcc63aae88300fb8ce049f9", "bytes": 55327, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/ijms.48244", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7484674", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE109651", "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=GSE109651", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE109651", "version": null, "note": "The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138+ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138+ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2947875", "GSM2947876", "GSM2947877", "GSM2947878", "GSM2947879", "GSM2947880", "GSM2947881", "GSM2947882", "GSM2947883", "GSM2947884", "GSM2947885", "GSM2947886", "GSM2947887", "GSM2947888"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression Profiles of Multiple Myeloma from the sorted SP/LC and CD138+ cells", "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:GSE2658", "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=GSE2658", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2658", "version": null, "note": "The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138+ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138+ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM102606", "GSM102607", "GSM102609", "GSM102610", "GSM102611", "GSM102612", "GSM102613", "GSM102614", "GSM102615", "GSM102616", "GSM102617", "GSM102618", "GSM102620", "GSM102621", "GSM102622", "GSM102623", "GSM102624", "GSM102625", "GSM102626", "GSM102627", "GSM102628", "GSM102629", "GSM102630", "GSM102631", "GSM102632", "GSM102633", "GSM102634", "GSM50986", "GSM50987", "GSM50988", "GSM50989", "GSM50990", "GSM50991", "GSM50992", "GSM50993", "GSM50994", "GSM50995", "GSM50996", "GSM50997", "GSM50998", "GSM50999", "GSM51000", "GSM51001", "GSM51002", "GSM51003", "GSM51004", "GSM51005", "GSM51006", "GSM51007", "GSM51008", "GSM51009", "GSM51010", "GSM51011", "GSM51012", "GSM51013", "GSM51014", "GSM51015", "GSM51016", "GSM51017", "GSM51018", "GSM51019", "GSM51020", "GSM51021", "GSM51022", "GSM51023", "GSM51024", "GSM51025", "GSM51026", "GSM51027", "GSM51028", "GSM51029", "GSM51030", "GSM51031", "GSM51032", "GSM51033", "GSM51034", "GSM51035", "GSM51036", "GSM51037", "GSM51038", "GSM51039", "GSM51040", "GSM51041", "GSM51042", "GSM51043", "GSM51044", "GSM51045", "GSM51046", "GSM51047", "GSM51048", "GSM51049", "GSM51050", "GSM51051", "GSM51052", "GSM51053", "GSM51054", "GSM51055", "GSM51056", "GSM51057", "GSM51058", "GSM51059", "GSM51060", "GSM51061", "GSM51062", "GSM51063", "GSM51064", "GSM51065", "GSM51066", "GSM51067", "GSM51068", "GSM51069", "GSM51070", "GSM51071", "GSM51072", "GSM51073", "GSM51074", "GSM51075", "GSM51076", "GSM51077", "GSM51078", "GSM51079", "GSM51080", "GSM51081", "GSM51082", "GSM51083", "GSM51084", "GSM51085", "GSM51086", "GSM51087", "GSM51088", "GSM51089", "GSM51090", "GSM51091", "GSM51092", "GSM51093", "GSM51094", "GSM51095", "GSM51096", "GSM51097", "GSM51098", "GSM51099", "GSM51100", "GSM51101", "GSM51102", "GSM51103", "GSM51104", "GSM51105", "GSM51106", "GSM51107", "GSM51108", "GSM51109", "GSM51110", "GSM51111", "GSM51112", "GSM51113", "GSM51114", "GSM51115", "GSM51116", "GSM51117", "GSM51118", "GSM51119", "GSM51120", "GSM51121", "GSM51122", "GSM51123", "GSM51124", "GSM51125", "GSM51126", "GSM51127", "GSM51128", "GSM51129", "GSM51130", "GSM51131", "GSM51132", "GSM51133", "GSM51134", "GSM51135", "GSM51136", "GSM51137", "GSM51138", "GSM51139", "GSM51140", "GSM51141", "GSM51142", "GSM51143", "GSM51144", "GSM51145", "GSM51146", "GSM51147", "GSM51148", "GSM51149", "GSM51150", "GSM51151", "GSM51152", "GSM51153", "GSM51154", "GSM51155", "GSM51156", "GSM51157", "GSM51158", "GSM51159", "GSM51160", "GSM51161", "GSM51162", "GSM51163", "GSM51164", "GSM51165", "GSM51166", "GSM51167", "GSM51168", "GSM51169", "GSM51170", "GSM51171", "GSM51172", "GSM51173", "GSM51174", "GSM51175", "GSM51176", "GSM51177", "GSM51178", "GSM51179", "GSM51180", "GSM51181", "GSM51182", "GSM51183", "GSM51184", "GSM51185", "GSM51186", "GSM51187", "GSM51188", "GSM51189", "GSM51190", "GSM51191", "GSM51192", "GSM51193", "GSM51194", "GSM51195", "GSM51196", "GSM51197", "GSM51198", "GSM51199", "GSM51200", "GSM51201", "GSM51202", "GSM51203", "GSM51204", "GSM51205", "GSM51206", "GSM51207", "GSM51208", "GSM51209", "GSM51210", "GSM51211", "GSM51212", "GSM51213", "GSM51214", "GSM51215", "GSM51216", "GSM51217", "GSM51218", "GSM51219", "GSM51220", "GSM51221", "GSM51222", "GSM51223", "GSM51224", "GSM51225", "GSM51226", "GSM51227", "GSM51228", "GSM51229", "GSM51230", "GSM51231", "GSM51232", "GSM51233", "GSM51234", "GSM51235", "GSM51236", "GSM51237", "GSM51238", "GSM51239", "GSM51240", "GSM51241", "GSM51242", "GSM51243", "GSM51244", "GSM51245", "GSM51246", "GSM51247", "GSM51248", "GSM51249", "GSM51250", "GSM51251", "GSM51252", "GSM51253", "GSM51254", "GSM51255", "GSM51256", "GSM51257", "GSM51258", "GSM51259", "GSM51260", "GSM51261", "GSM51262", "GSM51263", "GSM51264", "GSM51265", "GSM51266", "GSM51267", "GSM51268", "GSM51269", "GSM51270", "GSM51271", "GSM51272", "GSM51273", "GSM51274", "GSM51275", "GSM51276", "GSM51277", "GSM51278", "GSM51279", "GSM51280", "GSM51281", "GSM51282", "GSM51283", "GSM51284", "GSM51285", "GSM51286", "GSM51287", "GSM51288", "GSM51289", "GSM51290", "GSM51291", "GSM51292", "GSM51293", "GSM51294", "GSM51295", "GSM51296", "GSM51297", "GSM51298", "GSM51299", "GSM51300", "GSM51301", "GSM51302", "GSM51303", "GSM51304", "GSM51305", "GSM51306", "GSM51307", "GSM51308", "GSM51309", "GSM51310", "GSM51311", "GSM51312", "GSM51313", "GSM51314", "GSM51315", "GSM51316", "GSM51317", "GSM51318", "GSM51319", "GSM51320", "GSM51321", "GSM51322", "GSM51323", "GSM51324", "GSM51325", "GSM51326", "GSM51327", "GSM51328", "GSM51329", "GSM51330", "GSM51331", "GSM51332", "GSM51333", "GSM51334", "GSM51335", "GSM51336", "GSM95646", "GSM95647", "GSM95648", "GSM95649", "GSM95650", "GSM95651", "GSM95652", "GSM95653", "GSM95654", "GSM95655", "GSM95656", "GSM95657", "GSM95658", "GSM95659", "GSM95660", "GSM95661", "GSM95662", "GSM95663", "GSM95664", "GSM95665", "GSM95666", "GSM95667", "GSM95668", "GSM95669", "GSM95670", "GSM95671", "GSM95672", "GSM95673", "GSM95674", "GSM95675", "GSM95676", "GSM95677", "GSM95678", "GSM95679", "GSM95680", "GSM95681", "GSM95682", "GSM95683", "GSM95684", "GSM95685", "GSM95686", "GSM95687", "GSM95688", "GSM95689", "GSM95690", "GSM95691", "GSM95692", "GSM95693", "GSM95694", "GSM95695", "GSM95696", "GSM95697", "GSM95698", "GSM95699", "GSM95700", "GSM95701", "GSM95702", "GSM95703", "GSM95704", "GSM95705", "GSM95706", "GSM95707", "GSM95708", "GSM95709", "GSM95710", "GSM95711", "GSM95712", "GSM95713", "GSM95714", "GSM95715", "GSM95716", "GSM95717", "GSM95718", "GSM95719", "GSM95720", "GSM95721", "GSM95722", "GSM95723", "GSM95724", "GSM95725", "GSM95726", "GSM95727", "GSM95728", "GSM95729", "GSM95730", "GSM95731", "GSM95732", "GSM95733", "GSM95734", "GSM95735", "GSM95736", "GSM95737", "GSM95738", "GSM95739", "GSM95740", "GSM95741", "GSM95742", "GSM95743", "GSM95744", "GSM95745", "GSM95746", "GSM95747", "GSM95748", "GSM95749", "GSM95750", "GSM95751", "GSM95752", "GSM95753", "GSM95754", "GSM95755", "GSM95756", "GSM95757", "GSM95758", "GSM95759", "GSM95760", "GSM95761", "GSM95762", "GSM95763", "GSM95764", "GSM95765", "GSM95766", "GSM95767", "GSM95768", "GSM95769", "GSM95770", "GSM95771", "GSM95772", "GSM95773", "GSM95774", "GSM95775", "GSM95776", "GSM95777", "GSM95778", "GSM95779", "GSM95780", "GSM95781", "GSM95782", "GSM95783", "GSM95784", "GSM95785", "GSM95786", "GSM95787", "GSM95788", "GSM95789", "GSM95790", "GSM95791", "GSM95792", "GSM95793", "GSM95794", "GSM95795", "GSM95796", "GSM95797", "GSM95798", "GSM95799", "GSM95800", "GSM95801", "GSM95802", "GSM95803", "GSM95804", "GSM95805", "GSM95806", "GSM95807", "GSM95808", "GSM95809", "GSM95810", "GSM95811", "GSM95812", "GSM95813", "GSM95814", "GSM95815", "GSM95816", "GSM95817", "GSM95818", "GSM95819", "GSM95820", "GSM95821", "GSM95822", "GSM95823", "GSM95824", "GSM95825", "GSM95826"], "sample_count": 559, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression Profiles of Multiple Myeloma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32922167:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9ebb20fec49ab5e02a17be5873a3eca6b650d7b081d824b1a148b6694fef80f7", "bytes": 2343, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T4", "version": null, "note": "The top 5 significantly enriched GO terms and corresponding gene information in module analysis", "structure": {"pmcid": "PMC7484674", "section_index": 6, "section_title": "PPI network construction and modular analysis", "row_count": 16, "column_count": 7}, "table": {"label": "Table 4", "caption": "The top 5 significantly enriched GO terms and corresponding gene information in module analysis", "rows": [["Modules", "GO-ID", "P-value", "corr P-value", "x", "Description", "Genes in test set"], ["", "6952", "2.31E-16", "2.51E-13", "20", "defense response", "ORM1|CRISP3|ITGB2|HP|CYBB|RAB27A|CXCL1|FPR2|LILRB2|PLD1|CFP|CLEC4D|CLEC5A|C3AR1|LCN2|OLR1|PTX3|PGLYRP1|CAMP|LTF"], ["", "2376", "6.99E-13", "3.80E-10", "20", "immune system process", "ITGAM|ARG1|CRISP3|ITGB2|CYBB|RAB27A|CXCL1|LILRB2|CFP|MMP9|FCAR|CHIT1|BST1|CLEC4D|C3AR1|LCN2|PTX3|CEACAM8|PGLYRP1|LTF"], ["module 1", "6955", "1.24E-11", "4.49E-09", "16", "immune response", "ARG1|CRISP3|CYBB|RAB27A|CXCL1|LILRB2|CFP|FCAR|CHIT1|BST1|CLEC4D|LCN2|PTX3|CEACAM8|PGLYRP1|LTF"], ["", "5576", "3.52E-10", "9.56E-08", "24", "extracellular region", "ORM1|ARG1|CRISP3|HP|CXCL1|RETN|OLFM4|MMP8|CFP|MMP9|FCAR|CHIT1|TCN1|CEACAM1|SLPI|LCN2|OLR1|CHI3L1|PTX3|CEACAM8|FOLR3|PGLYRP1|CAMP|LTF"], ["", "30246", "6.48E-09", "1.38E-06", "11", "carbohydrate binding", "CHIT1|ITGAM|CLEC4D|CLEC12A|ARG1|CLEC5A|OLR1|CHI3L1|PTX3|PGLYRP1|LTF"], ["", "22403", "2.21E-18", "1.13E-15", "14", "cell cycle phase", "PLK1|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|RAD54L|OIP5|DLGAP5|CDKN3"], ["", "7049", "3.54E-18", "1.13E-15", "16", "cell cycle", "PLK1|HJURP|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|RAD54L|OIP5|DLGAP5|CDKN3|E2F8"], ["module 2", "87", "6.92E-18", "1.48E-15", "12", "M phase of mitotic cell cycle", "CDC20|CCNB2|ASPM|KIFC1|PLK1|CDK1|PBK|CDCA8|OIP5|CDC25C|NDC80|DLGAP5"], ["", "279", "9.72E-18", "1.56E-15", "13", "M phase", "PLK1|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|RAD54L|OIP5|DLGAP5"], ["", "278", "2.74E-17", "3.51E-15", "13", "mitotic cell cycle", "PLK1|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|OIP5|DLGAP5|CDKN3"], ["", "7186", "1.94E-08", "8.23E-06", "7", "G-protein coupled receptor protein signaling pathway", "CXCL12|CXCR1|CXCR2|PNOC|NMU|ADCY4|APLNR"], ["", "42330", "8.82E-08", "1.25E-05", "5", "taxis", "CXCL6|CXCL12|CXCR1|CCL5|CXCR2"], ["module 3", "6935", "8.82E-08", "1.25E-05", "5", "chemotaxis", "CXCL6|CXCL12|CXCR1|CCL5|CXCR2"], ["", "7610", "4.59E-07", "4.18E-05", "6", "behavior", "CXCL6|CXCL12|CXCR1|CCL5|CXCR2|NMU"], ["", "4918", "4.93E-07", "4.18E-05", "2", "interleukin-8 receptor activity", "CXCR1|CXCR2"]], "row_count": 16, "column_count": 7, "numeric_cells": 77, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:32922167:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8d10669cf7e84058c7de2a401977e458b49298080c4d083f216ccd54c85bd86b", "bytes": 1297, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Detailed information on the top 10 DEGs in the analysis", "structure": {"pmcid": "PMC7484674", "section_index": 10, "section_title": "Identification of DEGs", "row_count": 11, "column_count": 8}, "table": {"label": "Table 1", "caption": "Detailed information on the top 10 DEGs in the analysis", "rows": [["Symbol", "Name", "AveExpr", "t", "P-Value", "adj.P-Val", "B", "logFC"], ["SLC27A5", "solute carrier family 27 member 5", "6.641", "-9.704", "7.23E-08", "1.46E-03", "7.969", "-2.685"], ["MARCHF11", "membrane associated ring-CH-type finger 11", "4.541", "7.686", "1.38E-06", "1.16E-02", "5.451", "3.293"], ["RBFA", "ribosome binding factor A", "6.812", "-7.379", "2.26E-06", "1.16E-02", "5.015", "-3.401"], ["GFI1B", "growth factor independent 1B transcriptional repressor", "6.468", "-6.874", "5.21E-06", "1.16E-02", "4.267", "-4.616"], ["ECI2", "enoyl-CoA delta isomerase 2", "9.317", "-6.799", "5.91E-06", "1.16E-02", "4.152", "-3.099"], ["SNRK-AS1", "SNRK antisense RNA 1", "7.699", "6.755", "6.38E-06", "1.16E-02", "4.084", "2.448"], ["PTK2", "protein tyrosine kinase 2", "6.761", "-6.680", "7.25E-06", "1.16E-02", "3.968", "-3.842"], ["RPS6KL1", "ribosomal protein S6 kinase like 1", "6.489", "-6.673", "7.34E-06", "1.16E-02", "3.957", "-2.658"], ["LRRC45", "leucine rich repeat containing 45", "6.612", "-6.639", "7.78E-06", "1.16E-02", "3.903", "-2.562"], ["KBTBD7", "kelch repeat and BTB domain containing 7", "10.589", "6.635", "7.83E-06", "1.16E-02", "3.898", "2.122"]], "row_count": 11, "column_count": 8, "numeric_cells": 72, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32922167:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5af6fa5212a7ab2290a79499c8cce318e7747cc0879face0f849f4ceb38383cf", "bytes": 2292, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "Gene Ontology term enrichment analysis of DEGs in LC/SP cells of MM.", "structure": {"pmcid": "PMC7484674", "section_index": 11, "section_title": "GO term enrichment analysis of DEGs", "row_count": 31, "column_count": 6}, "table": {"label": "Table 2", "caption": "Gene Ontology term enrichment analysis of DEGs in LC/SP cells of MM.", "rows": [["Expression", "Category", "ID", "Term", "Count", "PValue"], ["", "BP", "GO:0045087", "innate immune response", "28", "3.13E-09"], ["", "BP", "GO:0006954", "inflammatory response", "25", "2.07E-08"], ["", "BP", "GO:0006955", "immune response", "20", "8.02E-05"], ["", "BP", "GO:0006691", "leukotriene metabolic process", "5", "8.69E-05"], ["", "BP", "GO:0030593", "neutrophil chemotaxis", "8", "1.07E-04"], ["", "CC", "GO:0005886", "plasma membrane", "122", "1.23E-11"], ["", "CC", "GO:0016021", "integral component of membrane", "131", "5.17E-08"], ["UP-DEGs", "CC", "GO:0005615", "extracellular space", "48", "1.22E-06"], ["", "CC", "GO:0042581", "specific granule", "6", "1.47E-06"], ["", "CC", "GO:0005887", "integral component of plasma membrane", "46", "2.27E-05"], ["", "MF", "GO:0030246", "carbohydrate binding", "12", "4.29E-04"], ["", "MF", "GO:0005509", "calcium ion binding", "24", "1.91E-03"], ["", "MF", "GO:0050544", "arachidonic acid binding", "3", "2.63E-03"], ["", "MF", "GO:0004198", "calcium-dependent cysteine-type endopeptidase activity", "4", "4.76E-03"], ["", "MF", "GO:0005536", "glucose binding", "3", "1.36E-02"], ["", "BP", "GO:0006782", "protoporphyrinogen IX biosynthetic process", "5", "1.81E-05"], ["", "BP", "GO:0006783", "heme biosynthetic process", "6", "4.80E-05"], ["", "BP", "GO:0030218", "erythrocyte differentiation", "7", "1.31E-04"], ["", "BP", "GO:0006779", "porphyrin-containing compound biosynthetic process", "4", "4.09E-04"], ["", "BP", "GO:0008283", "cell proliferation", "19", "4.20E-04"], ["", "CC", "GO:0070062", "extracellular exosome", "84", "2.77E-05"], ["", "CC", "GO:0005833", "hemoglobin complex", "5", "5.86E-05"], ["DOWN-DEGs", "CC", "GO:0014731", "spectrin-associated cytoskeleton", "4", "3.66E-04"], ["", "CC", "GO:0015629", "actin cytoskeleton", "13", "1.08E-03"], ["", "CC", "GO:0005739", "mitochondrion", "42", "1.84E-03"], ["", "MF", "GO:0034987", "immunoglobulin receptor binding", "5", "1.51E-03"], ["", "MF", "GO:0005344", "oxygen transporter activity", "4", "2.28E-03"], ["", "MF", "GO:0004029", "aldehyde dehydrogenase (NAD) activity", "4", "4.07E-03"], ["", "MF", "GO:0051015", "actin filament binding", "9", "4.36E-03"], ["", "MF", "GO:0004064", "arylesterase activity", "3", "5.39E-03"]], "row_count": 31, "column_count": 6, "numeric_cells": 90, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32922167:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3ed3c14c66997a679798f6661f84acb8765dfccd787f08fa3f541e218e725e4a", "bytes": 899, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T3", "version": null, "note": "KEGG pathway enrichment analysis of DEGs in LC/SP cells of MM", "structure": {"pmcid": "PMC7484674", "section_index": 12, "section_title": "KEGG pathway enrichment analysis of DEGs", "row_count": 11, "column_count": 5}, "table": {"label": "Table 3", "caption": "KEGG pathway enrichment analysis of DEGs in LC/SP cells of MM", "rows": [["Expression", "Category", "Term", "Count", "P-Value"], ["", "hsa04380", "Osteoclast differentiation", "11", "1.50E-04"], ["", "hsa04060", "Cytokine-cytokine receptor interaction", "14", "5.51E-04"], ["UP-DEGs", "hsa05150", "Staphylococcus aureus infection", "6", "3.15E-03"], ["", "hsa04670", "Leukocyte transendothelial migration", "8", "5.44E-03"], ["", "hsa04514", "Cell adhesion molecules (CAMs)", "8", "1.64E-02"], ["", "hsa00860", "Porphyrin and chlorophyll metabolism", "7", "1.63E-04"], ["", "hsa04640", "Hematopoietic cell lineage", "8", "1.65E-03"], ["DOWN-DEGs", "hsa01100", "Metabolic pathways", "39", "2.24E-03"], ["", "hsa01130", "Biosynthesis of antibiotics", "12", "3.24E-03"], ["", "hsa04110", "Cell cycle", "8", "1.16E-02"]], "row_count": 11, "column_count": 5, "numeric_cells": 30, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:32922167:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9ebb20fec49ab5e02a17be5873a3eca6b650d7b081d824b1a148b6694fef80f7", "bytes": 2343, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T4", "version": null, "note": "The top 5 significantly enriched GO terms and corresponding gene information in module analysis", "structure": {"pmcid": "PMC7484674", "section_index": 13, "section_title": "PPI network construction and modular analysis", "row_count": 16, "column_count": 7}, "table": {"label": "Table 4", "caption": "The top 5 significantly enriched GO terms and corresponding gene information in module analysis", "rows": [["Modules", "GO-ID", "P-value", "corr P-value", "x", "Description", "Genes in test set"], ["", "6952", "2.31E-16", "2.51E-13", "20", "defense response", "ORM1|CRISP3|ITGB2|HP|CYBB|RAB27A|CXCL1|FPR2|LILRB2|PLD1|CFP|CLEC4D|CLEC5A|C3AR1|LCN2|OLR1|PTX3|PGLYRP1|CAMP|LTF"], ["", "2376", "6.99E-13", "3.80E-10", "20", "immune system process", "ITGAM|ARG1|CRISP3|ITGB2|CYBB|RAB27A|CXCL1|LILRB2|CFP|MMP9|FCAR|CHIT1|BST1|CLEC4D|C3AR1|LCN2|PTX3|CEACAM8|PGLYRP1|LTF"], ["module 1", "6955", "1.24E-11", "4.49E-09", "16", "immune response", "ARG1|CRISP3|CYBB|RAB27A|CXCL1|LILRB2|CFP|FCAR|CHIT1|BST1|CLEC4D|LCN2|PTX3|CEACAM8|PGLYRP1|LTF"], ["", "5576", "3.52E-10", "9.56E-08", "24", "extracellular region", "ORM1|ARG1|CRISP3|HP|CXCL1|RETN|OLFM4|MMP8|CFP|MMP9|FCAR|CHIT1|TCN1|CEACAM1|SLPI|LCN2|OLR1|CHI3L1|PTX3|CEACAM8|FOLR3|PGLYRP1|CAMP|LTF"], ["", "30246", "6.48E-09", "1.38E-06", "11", "carbohydrate binding", "CHIT1|ITGAM|CLEC4D|CLEC12A|ARG1|CLEC5A|OLR1|CHI3L1|PTX3|PGLYRP1|LTF"], ["", "22403", "2.21E-18", "1.13E-15", "14", "cell cycle phase", "PLK1|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|RAD54L|OIP5|DLGAP5|CDKN3"], ["", "7049", "3.54E-18", "1.13E-15", "16", "cell cycle", "PLK1|HJURP|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|RAD54L|OIP5|DLGAP5|CDKN3|E2F8"], ["module 2", "87", "6.92E-18", "1.48E-15", "12", "M phase of mitotic cell cycle", "CDC20|CCNB2|ASPM|KIFC1|PLK1|CDK1|PBK|CDCA8|OIP5|CDC25C|NDC80|DLGAP5"], ["", "279", "9.72E-18", "1.56E-15", "13", "M phase", "PLK1|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|RAD54L|OIP5|DLGAP5"], ["", "278", "2.74E-17", "3.51E-15", "13", "mitotic cell cycle", "PLK1|CDCA8|CDC25C|NDC80|CDC20|CCNB2|ASPM|KIFC1|CDK1|PBK|OIP5|DLGAP5|CDKN3"], ["", "7186", "1.94E-08", "8.23E-06", "7", "G-protein coupled receptor protein signaling pathway", "CXCL12|CXCR1|CXCR2|PNOC|NMU|ADCY4|APLNR"], ["", "42330", "8.82E-08", "1.25E-05", "5", "taxis", "CXCL6|CXCL12|CXCR1|CCL5|CXCR2"], ["module 3", "6935", "8.82E-08", "1.25E-05", "5", "chemotaxis", "CXCL6|CXCL12|CXCR1|CCL5|CXCR2"], ["", "7610", "4.59E-07", "4.18E-05", "6", "behavior", "CXCL6|CXCL12|CXCR1|CCL5|CXCR2|NMU"], ["", "4918", "4.93E-07", "4.18E-05", "2", "interleukin-8 receptor activity", "CXCR1|CXCR2"]], "row_count": 16, "column_count": 7, "numeric_cells": 77, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:32922167:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6aa65f4bc94f525a827c06f5ec5fdc7b7b549ee501e2828caa8f2cb0bfa72b94", "bytes": 1558, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T5", "version": null, "note": "The top 10 hub genes and their most relevant functions", "structure": {"pmcid": "PMC7484674", "section_index": 14, "section_title": "Selection of hub genes from the PPI network", "row_count": 11, "column_count": 5}, "table": {"label": "Table 5", "caption": "The top 10 hub genes and their most relevant functions", "rows": [["Symbol", "Gene name", "Degree", "Relevant function", "Reference"], ["ITGAM", "integrin subunit alpha M", "78", "A poor prognostic factor in MM and AML patients;", "57-61"], ["MMP9", "Matrix metallopeptidase 9", "64", "Participates in the breakdown of extracellular matrix; Promotes invasion of MM;", "73, 79-84"], ["ITGB2", "Integrin subunit beta 2", "62", "Involved in cell adhesion and cell-surface mediated signaling;Associated with drug resistance to chemotherapy in MM cell line;", "63, 66"], ["FPR2", "Formyl-peptide receptor-2", "52", "Associated with invasion and metastasis of some cancers;", "96-98"], ["C3AR1", "complement C3a receptor 1", "51", "Involved in drug resistance to chemotherapy in AML cell;Predicts overall survival of AML;", "99"], ["CXCL1", "C-X-C motif chemokine ligand 1", "51", "Associated with the growth and progression of some cancers;", "100-102"], ["CYBB", "cytochrome b-245 beta chain", "48", "Involved in the progression of some cancers by promotion of angiogenesis;", "103, 104"], ["LILRB2", "leukocyte immunoglobulin like receptor B2", "46", "Inhibits stimulation of an immune response; Promotes tumor progression;", "105-107"], ["HP", "haptoglobin", "44", "NA", "-"], ["FCER1G", "Fc fragment of IgE receptor Ig", "43", "Associated with disease progression in lymphoma and some solid cancers;Deficient expression represents T-cell immunodeficiency in CLL.", "108-110"]], "row_count": 11, "column_count": 5, "numeric_cells": 25, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:32922167:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:44a716ac1f581a61b3fbdca3938d9df9b9fded60ad579cb3b8e16034905b2d93", "bytes": 763, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T6", "version": null, "note": "Multivariate Cox regression analysis of 9 genes used for constructing the prognostic model", "structure": {"pmcid": "PMC7484674", "section_index": 15, "section_title": "Survival analysis of DEGs", "row_count": 10, "column_count": 6}, "table": {"label": "Table 6", "caption": "Multivariate Cox regression analysis of 9 genes used for constructing the prognostic model", "rows": [["Symbol", "Coefficient", "HR", "Lower 95%CI", "Upper 95%CI", "P-value"], ["TFF3", "0.566", "1.762", "1.240", "2.503", "0.002"], ["EPDR1", "0.492", "1.636", "1.132", "2.364", "0.009"], ["MACROD1", "0.745", "2.107", "1.189", "3.734", "0.011"], ["ARHGEF12", "-0.540", "0.583", "0.389", "0.874", "0.009"], ["AMMECR1", "0.862", "2.369", "1.142", "4.913", "0.020"], ["NFATC2", "0.679", "1.972", "1.258", "3.090", "0.003"], ["HES6", "0.513", "1.671", "1.091", "2.560", "0.018"], ["PLEK2", "0.527", "1.694", "1.041", "2.758", "0.034"], ["SNCA", "0.759", "2.135", "1.216", "3.749", "0.008"]], "row_count": 10, "column_count": 6, "numeric_cells": 48, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T6"}}], "gaps": ["asset:data:geo:GSE109651 not downloaded", "asset:data:geo:GSE109651 licence not read", "asset:data:geo:GSE2658 not downloaded", "asset:data:geo:GSE2658 licence not read"]}, "analysis": {"state": "partial", "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": "Then, DEGs between LC/SP cells and MP CD138+ cells of MM were identified by an empirical Bayes method based on the “limma” package in R."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox proportional hazards"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-5", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-6", "family": "network_analysis", "specific": "centrality", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "centrality"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE109651", "GSE2658"], "resolved_accessions": ["GSE109651", "GSE2658"], "statements": ["The gene expression dataset GSE109651 was obtained from GEO database. The microarray data of GSE109651, based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133A Plus 2.0 Array) and normalized using the MAS5 algorithm of the Affymetrix expression console version1.1 software (Affymetrix), includes 7-paired LC/SP cells and MP CD138+ cells of myeloma bone marrow from 7 diagnosed MM patients isolated by fluorescence-activated cell sorting (FACS) using Hoechst 33342 and CD138 antibody."], "basis": "The paper names GSE109651, GSE2658 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32922167", "data:geo:GSE109651", "asset:table:pmid:32922167:1", "asset:table:pmid:32922167:2", "asset:table:pmid:32922167:3", "asset:table:pmid:32922167:4", "asset:table:pmid:32922167:5", "asset:table:pmid:32922167:6", "asset:table:pmid:32922167:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE109651"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 45780, "completion_tokens": 1531, "cached_tokens": 776}}, "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:32922167", "type": "paper", "label": "pmid:32922167"}, {"id": "source:pmid:32922167", "type": "manuscript", "label": "PMID 32922167 full text"}, {"id": "data:geo:GSE109651", "type": "dataset", "label": "GEO GSE109651"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32922167", "type": "paper", "label": "pmid:32922167"}, {"id": "source:pmid:32922167", "type": "manuscript", "label": "PMID 32922167 full text"}, {"id": "data:geo:GSE109651", "type": "dataset", "label": "GEO GSE109651"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32922167", "type": "extraction", "used": ["source:pmid:32922167"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE109651", "type": "accession_resolution", "used": ["data:geo:GSE109651"], "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:32922167", "parent_hash": "sha256:d98cf6e81110da51a9a71b7f6677ff8333520e4160809b0110663b3021b62db9", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE109651 licence not read", "asset:data:geo:GSE109651 not downloaded", "asset:data:geo:GSE2658 licence not read", "asset:data:geo:GSE2658 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Then, DEGs between LC/SP cells and MP CD138+ cells of MM were identified by an empirical Bayes method based on the “limma” package in R."], "order_basis": "analysis_only", "id": "assay:1"}]}