← All .science files
pmid:32195281
RNA-Seq Bayesian Network Exploration of Immune System in Bovine.
Elham Behdani · Mostafa Ghaderi-Zefrehei · Farjad Rafeie · Mohammad Reza Bakhtiarizadeh · Hedayatollah Roshanfeker · Jamal Fayazi
Iranian journal of biotechnology · 2019 doi:10.29252/ijb.1748
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 · 6 items
claims array · 2 items
[0] object · 6 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 · 6 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 48 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 3 items
[0] array · 1 item
[1] array · 7 items
[2] array · 7 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 5 items
[0] array · 8 items
[1] array · 8 items
[2] array · 8 items
[3] array · 8 items
[4] array · 8 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 15 items
[0] array · 9 items
[1] array · 9 items
[2] array · 9 items
[3] array · 9 items
[4] array · 9 items
[5] array · 9 items
[6] array · 9 items
[7] array · 9 items
[8] array · 9 items
[9] array · 9 items
[10] array · 9 items
[11] array · 9 items
[12] array · 9 items
[13] array · 9 items
[14] array · 9 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
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 · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 6 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 · 1 item
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 · 7 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32195281", "kind": "science-record", "revision": 5, "content_hash": "sha256:c7f0cb01ed0630200e019b0871e90968136f850d48fd8d551b009f955b9ec5d9", "created_at": "2026-11-01T15:40:58Z", "updated_at": "2026-11-01T21:23:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RNA-Seq Bayesian Network Exploration of Immune System in Bovine.", "doi": "10.29252/ijb.1748", "pmid": "32195281", "authors": ["Elham Behdani", "Mostafa Ghaderi-Zefrehei", "Farjad Rafeie", "Mohammad Reza Bakhtiarizadeh", "Hedayatollah Roshanfeker", "Jamal Fayazi"], "journal": "Iranian journal of biotechnology", "year": 2019, "abstract": "BACKGROUND: The stress is one of main factors effects on production system. Several factors (both genetic and environmental elements) regulate immune response to stress.\nOBJECTIVES: In order to determine the major immune system regulatory genes underlying stress responses, a learning Bayesian network approach for those regulatory genes was applied to RNA-Seq data from a bovine leukocyte model system.\nMATERIAL AND METHODS: The transcriptome dataset GSE37447 was used from GEO and a Bayesian network on differentially expressed genes was learned to investigate the gene regulatory network.\nRESULTS: Applying the method produced a strongly interconnected network with four genes (TERF2IP, PDCD10, DDX10 and CENPE) acting as nodes, suggesting these genes may be important in the transcriptome regulation program of stress response. Of these genes TERF2IP has been shown previously to regulate gene expression, act as a regulator of the nuclear factor-kappa B (NF-κB) signalling, and to activate expression of NF-κB target genes; PDCD10 encodes a conserved protein associated with cell apoptosis; DDX10 encodes a DEAD box protein and is believed to be associated with cellular growth and division; and CENPE involves unstable spindle microtubule capture at kinetochores. Together these genes are involved in DNA damage of apoptosis, RNA splicing, DNA repairing, and regulating cell division in the bovine genome. The topology of the learned Bayesian gene network indicated that the genes had a minimal interrelationship with each other. This type of structure, using the publically available computational tool, was also observed on human orthologous genes of the differentially expressed genes.\nCONCLUSIONS: Overall, the results might be used in transcriptomic-assisted selection and design of new drug targets to treat stress-related problems in bovines.", "claims": [{"id": "claim-method", "statement": "To investigate the gene regulatory network, a Bayesian network on differentially expressed genes was learned using the networkBMA package ( 19 ).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32195281", "locator": "sections[5] \"3.2. RNA-Seq Bayesian Network\" paragraph 2", "quote": "To investigate the gene regulatory network, a Bayesian network on differentially expressed genes was learned using the networkBMA package ( 19 )."}], "state": "complete"}, {"id": "claim-data-access", "statement": "This data was respect to RNA-Seq leukocyte of male beef calves in response to weaning stress over different days (0, 1, 2 and 7 d).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32195281", "locator": "sections[4] \"3.1. RNA-Seq Dataset Processing\" paragraph 2", "quote": "This data was respect to RNA-Seq leukocyte of male beef calves in response to weaning stress over different days (0, 1, 2 and 7 d)."}], "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:32195281"], "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:GSE37447"], "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:GSE37447"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32195281", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.29252/ijb.1748", "sha256": "sha256:2b672d1f50b966c155b59d6c029b4a3df0fe13e03616d7c0a88842b015bc38ab", "bytes": 24748, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.29252/ijb.1748", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7080973", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37447", "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=GSE37447", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37447", "version": null, "note": "This data was respect to RNA-Seq leukocyte of male beef calves in response to weaning stress over different days (0, 1, 2 and 7 d).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This data was respect to RNA-Seq leukocyte of male beef calves in response to weaning stress over different days (0, 1, 2 and 7 d).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM919456", "GSM919457", "GSM919458", "GSM919459", "GSM919460", "GSM919461", "GSM919462", "GSM919463", "GSM919464", "GSM919465", "GSM919466", "GSM919467", "GSM919468", "GSM919469", "GSM919470", "GSM919471", "GSM919472", "GSM919473", "GSM919474", "GSM919475", "GSM919476", "GSM919477", "GSM919478", "GSM919479", "GSM919480", "GSM919481", "GSM919482", "GSM919483", "GSM919484", "GSM919485", "GSM919486", "GSM919487", "GSM919488", "GSM919489", "GSM919490", "GSM919491", "GSM919492", "GSM919493", "GSM919494", "GSM919495", "GSM919496", "GSM919497", "GSM919498", "GSM919499", "GSM919500", "GSM919501", "GSM919502", "GSM919503"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "11153", "taxon": "Bos taurus", "title": "Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology", "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:32195281:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:98778ae6bdce8c9f644829a3f3c2ebbb87bdefb5c5300b9df93e1ef6b7a5c2f1", "bytes": 380, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#T1", "version": null, "note": "Statistical parameters of Bayesian gene regulatory network", "structure": {"pmcid": "PMC7080973", "section_index": 6, "section_title": "4. Results", "row_count": 3, "column_count": 7}, "table": {"label": "Table 1", "caption": "Statistical parameters of Bayesian gene regulatory network", "rows": [["Statistical parameters"], ["", "Density", "Connectivity", "Diameter", "Radius", "Shortest path", "Clustering coefficient"], ["Bayesian network", "0", "4.38", "6", "1", "1343", "0.160024"]], "row_count": 3, "column_count": 7, "numeric_cells": 6, "header_rows": 1, "locator": "section[6]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32195281:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:143e49663561fd3e302117506b8e21fc4ed9e3208bfcedbb90ae97e474c0482c", "bytes": 282, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[2]#T2", "version": null, "note": "Structure of network paths", "structure": {"pmcid": "PMC7080973", "section_index": 6, "section_title": "4. Results", "row_count": 2, "column_count": 7}, "table": {"label": "Table 2", "caption": "Structure of network paths", "rows": [["Shortest path length", "1", "2", "3", "4", "5", "6"], ["Number of shortest path", "424", "564", "203", "83", "67", "2"]], "row_count": 2, "column_count": 7, "numeric_cells": 12, "header_rows": 1, "locator": "section[6]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:32195281:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1bbde0b1f640372bd4de312e4e44bf114451271804b778da8a3420ba950fe638", "bytes": 672, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[3]#T3", "version": null, "note": "The network parameters of the most connected genes in GSE37447 experiment", "structure": {"pmcid": "PMC7080973", "section_index": 6, "section_title": "4. Results", "row_count": 5, "column_count": 8}, "table": {"label": "Table 3", "caption": "The network parameters of the most connected genes in GSE37447 experiment", "rows": [["Gene (Ensemble ID)", "Gene name", "Clustering coefficient", "Out- degree", "In-degree", "Neighbors connectivity", "Betweenness centrality", "Closeness centrality"], ["ENSBTAG00000015686", "TERF2IP", "0.003", "155", "5", "3.069", "0.016", "0.852"], ["ENSBTAG00000031709", "PDDCD10", "0.003", "94", "3", "3.546", "0.009", "0.446"], ["ENSBTAG00000002382", "DDX10", "0.019", "68", "0", "6.224", "0.000", "0.601"], ["ENSBTAG00000009035", "CENPE", "0.001", "64", "0", "2.635", "0.000", "1.000"]], "row_count": 5, "column_count": 8, "numeric_cells": 30, "header_rows": 1, "locator": "section[6]/table-wrap[3]#T3"}}, {"id": "asset:table:pmid:32195281:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d6860d68258af5453814a7acec30f0dfa84f42b11744eb4199fdee7a8c6c9337", "bytes": 1480, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[4]#T4", "version": null, "note": "The network parameters of most connected genes inferred from BioGrid repository", "structure": {"pmcid": "PMC7080973", "section_index": 6, "section_title": "4. Results", "row_count": 15, "column_count": 9}, "table": {"label": "Table 4", "caption": "The network parameters of most connected genes inferred from BioGrid repository", "rows": [["Gene", "Degree", "Radiality", "Closeness", "Stress", "Betweenness", "Centroid value", "Eccentricity", "Collective influence"], ["STK24", "1", "1.203846", "0.025281", "0.000000", "0.000000", "-204", "0.250000", "0"], ["PDCD10 *", "53", "1.988462", "0.035433", "0.476513", "0.476513", "-100", "0.333333", "7852"], ["STK25", "1", "1.203846", "0.025281", "0.000000", "0.000000", "-204", "0.250000", "0"], ["AP2B1", "1", "1.965385", "0.035019", "0.000000", "0.000000", "-204", "0.250000", "0"], ["TERF2IP *", "153", "2.750000", "0.058065", "1.000000", "1.000000", "98", "0.333333", "7852"], ["BUB1B", "1", "0.407692", "0.26087", "0.000000", "0.000000", "-34", "0.50000", "0"], ["CENPE *", "36", "0.538462", "0.514286", "0.030546", "0.030546", "34", "1.000000", "0"], ["FGFR1OP2", "1", "1.203846", "0.025281", "0.000000", "0.000000", "-204", "0.250000", "0"], ["TRAF3IP3", "1", "1.203846", "0.025281", "0.000000", "0.000000", "-204", "0.250000", "0"], ["G3BP2", "1", "0.211538", "0.514286", "0.000000", "0.000000", "-17", "0.500000", "0"], ["DDX10 *", "18", "0.276923", "1.000000", "0.007855", "0.007855", "17", "1.000000", "0"], ["SLX4", "1", "1.965385", "0.035019", "0.000000", "0.000000", "-204", "0.250000", "0"], ["PRC1", "1", "0.407692", "0.26087", "0.000000", "0.000000", "-34", "0.500000", "0"], ["MAPK1", "1", "0.407692", "0.26087", "0.000000", "0.000000", "-34", "0.500000", "0"]], "row_count": 15, "column_count": 9, "numeric_cells": 116, "header_rows": 1, "locator": "section[6]/table-wrap[4]#T4"}}], "gaps": ["asset:data:geo:GSE37447 not downloaded", "asset:data:geo:GSE37447 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Bayesian network learned with the networkBMA package", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To investigate the gene regulatory network, a Bayesian network on differentially expressed genes was learned using the networkBMA package ( 19 )."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Bayesian network learned with the networkBMA package), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE37447"], "resolved_accessions": ["GSE37447"], "statements": ["This data was respect to RNA-Seq leukocyte of male beef calves in response to weaning stress over different days (0, 1, 2 and 7 d)."], "basis": "The paper names GSE37447 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32195281", "data:geo:GSE37447", "asset:table:pmid:32195281:1", "asset:table:pmid:32195281:2", "asset:table:pmid:32195281:3", "asset:table:pmid:32195281:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE37447"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:54Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 16879, "completion_tokens": 1183, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32195281", "type": "paper", "label": "pmid:32195281"}, {"id": "source:pmid:32195281", "type": "manuscript", "label": "PMID 32195281 full text"}, {"id": "data:geo:GSE37447", "type": "dataset", "label": "GEO GSE37447"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32195281", "type": "paper", "label": "pmid:32195281"}, {"id": "source:pmid:32195281", "type": "manuscript", "label": "PMID 32195281 full text"}, {"id": "data:geo:GSE37447", "type": "dataset", "label": "GEO GSE37447"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32195281", "type": "extraction", "used": ["source:pmid:32195281"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE37447", "type": "accession_resolution", "used": ["data:geo:GSE37447"], "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:32195281", "parent_hash": "sha256:17ee1be2a96a6a3386007479c7f861c8bb9accc580cc07c5a0caae1694ac05f0", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE37447 licence not read", "asset:data:geo:GSE37447 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["RNA-Seq Bayesian Network Exploration of Immune Syste", "ch for those regulatory genes was applied to RNA-Seq data from a bovine leukocyte model system. M", "cyte model system. MATERIAL AND METHODS: The transcriptome dataset GSE37447 was used from GEO and a Bay", "ggesting these genes may be important in the transcriptome regulation program of stress response. Of th"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["des a conserved protein associated with cell apoptosis; DDX10 encodes a DEAD box protein and is bel", "er these genes are involved in DNA damage of apoptosis, RNA splicing, DNA repairing, and regulating"], "order_basis": "paper_text_order:1105", "id": "assay:2"}]}