Genome wide transcription profiling reveals a major role for the transcription factor Atf1 in regulation of cell division in Schizosaccharomyces pombe.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697368", "kind": "science-record", "revision": 6, "content_hash": "sha256:e2f0afb0948fdebfd75f6f74dc14fd7d8cfdc18f634b130007935a2429365fe2", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:20:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome wide transcription profiling reveals a major role for the transcription factor Atf1 in regulation of cell division in Schizosaccharomyces pombe.", "doi": "10.1016/j.gdata.2015.09.014", "pmid": "26697368", "authors": ["Sushobhana Bandyopadhyay", "Geetanjali Sundaram"], "journal": "Genomics data", "year": 2015, "abstract": "The mechanism underlying stringently controlled sequence of events in the eukaryotic cell cycle involves periodic transcription of a number of genes encoding important regulators of cell cycle, growth, proliferation and apoptosis. Deregulated activities of transcription factors that contribute to this programmed gene expression, are associated with many diseases including cancer. A detailed mechanistic understanding of the transcriptional control associated with cell division is, therefore, important. We have reported earlier that the transcription factor Atf1 in Schizosaccharomyces pombe can regulate G2-M transition by directly controlling the expression of the mitotic cyclin Cdc13 (1).To gain a better understanding of the role of Atf1 in cell cycle, we performed a microarray based identification of cell cycle related targets of Atf1. The microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series (accession number GSE71820). Here we report the annotation of the genes whose expression get altered by Atf1 overexpression and also provide details related to sample processing and statistical analysis of our microarray data.", "claims": [{"id": "claim-method", "statement": "The moderated t-test method was applied for assessing the statistically significant differentially expressed genes between the control sample (not overexpressing Atf1) and the sample in which Atf1 was overexpressed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697368", "locator": "sections[11] \"Differential gene expression analysis\" paragraph 2", "quote": "The moderated t-test method was applied for assessing the statistically significant differentially expressed genes between the control sample (not overexpressing Atf1) and the sample in which Atf1 was overexpressed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series (accession number GSE71820).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697368", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series (accession number GSE71820)."}], "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:26697368"], "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:GSE71820"], "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:GSE71820"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26697368", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.09.014", "sha256": "sha256:092317219dfc1b1d62602ddd0f201c0fbc8ab339c0e0ff7fecb200a1f8643f90", "bytes": 12420, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.09.014", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4664745", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE71820", "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=GSE71820", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71820", "version": null, "note": "The microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series (accession number GSE71820).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series (accession number GSE71820).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1846378", "GSM1846379", "GSM1846380", "GSM1846381"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "2529", "taxon": "Saccharomyces cerevisiae; Schizosaccharomyces pombe", "title": "Atf1 overexpression gene expression changesS. pombe", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26697368:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e9e12ddde3b767f45b3b6b920973eed78b1d29cb98b917dad678cfd6fa43d848", "bytes": 840, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC4664745", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Schizosaccharomyces pombe"], ["Sex", "Not Applicable"], ["Sequencer or array type", "Affymetrix-GeneChip® Yeast Genome 2.0 Array"], ["Data format", "Raw"], ["Experimental factors", "Atf1 was overexpressed in wild type S. pombe cells and gene expression in such cells was compared to that of control cells (which do not overexpress Atf1)"], ["Experimental features", "Cells were grown to saturation in the presence of 20 μM Thiamine. Thwy were then harvested, washed (to remove Thiamine) and resuspended in fresh media and incubated for 24 h before proceeding with RNA isolation"], ["Consent", "Not Applicable"], ["Sample source location", "Not Applicable"]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0015"}}], "gaps": ["asset:data:geo:GSE71820 not downloaded", "asset:data:geo:GSE71820 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "moderated t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The moderated t-test method was applied for assessing the statistically significant differentially expressed genes between the control sample (not overexpressing Atf1) and the sample in which Atf1 was overexpressed."}}], "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 (moderated t-test), 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": ["GSE71820"], "resolved_accessions": ["GSE71820"], "statements": ["The microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series (accession number GSE71820)."], "basis": "The paper names GSE71820 in NCBI's Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26697368", "data:geo:GSE71820", "asset:table:pmid:26697368:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE71820"]}, "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": "2026-10-31T18:06:59Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 10105, "completion_tokens": 947, "cached_tokens": 648}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:26697368", "type": "paper", "label": "pmid:26697368"}, {"id": "source:pmid:26697368", "type": "manuscript", "label": "PMID 26697368 full text"}, {"id": "data:geo:GSE71820", "type": "dataset", "label": "GEO GSE71820"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26697368", "type": "paper", "label": "pmid:26697368"}, {"id": "source:pmid:26697368", "type": "manuscript", "label": "PMID 26697368 full text"}, {"id": "data:geo:GSE71820", "type": "dataset", "label": "GEO GSE71820"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26697368", "type": "extraction", "used": ["source:pmid:26697368"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE71820", "type": "accession_resolution", "used": ["data:geo:GSE71820"], "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:26697368", "parent_hash": "sha256:92a627471b7b3c9c91bcebe8de3c0833d8aa441f56039c3600d57aa600973804", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE71820 licence not read", "asset:data:geo:GSE71820 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ors of cell cycle, growth, proliferation and apoptosis. Deregulated activities of transcription fac"], "order_basis": "paper_text_order:327", "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": 0.99, "evidence": ["e role of Atf1 in cell cycle, we performed a microarray based identification of cell cycle related t", "n of cell cycle related targets of Atf1. The microarray data are available at NCBI's Gene Expression", "e processing and statistical analysis of our microarray data.", "ufacturer's protocol. The array used in this microarray was Affymetrix-Gene Chip Yeast Genome 2.0 (A"], "order_basis": "paper_text_order:884", "id": "assay:2"}]}