Plasmodium falciparum epigenome: A distinct dynamic epigenetic regulation of gene expression.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981368", "kind": "science-record", "revision": 7, "content_hash": "sha256:7ceaa926501d17a4d2f51cfb2156b9df80b11a3aa21a3a4d6bbde06bb30b45d7", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:58:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Plasmodium falciparum epigenome: A distinct dynamic epigenetic regulation of gene expression.", "doi": "10.1016/j.gdata.2015.11.026", "pmid": "26981368", "authors": ["Mukul Rawat", "Madhvi A Bhosale", "Krishanpal Karmodiya"], "journal": "Genomics data", "year": 2016, "abstract": "Histone modification profiles are predictive of gene expression and most of the knowledge gained is acquired through studies done in higher eukaryotes. However, genome-wide studies involving Plasmodium falciparum, the causative agent of malaria, have been rather few, at lower resolution (mostly using ChIP-on-chip), and covering limited number of histone modifications. In our recent study [1], we have performed extensive genome-wide analyses of multiple histone modifications including the active (H3K4me2, H3K4me3, H3K9ac, H3K14ac, H3K27ac and H4ac), inactive (H3K9me3 and H3K27me3), elongation (H3K79me3) and regulatory element (H3K4me1) in a stage-specific manner. Furthermore, we used a ligation-based method suitable for sequencing homopolymeric stretches as seen in P. falciparum for next-generation sequencing library amplification [2], enabling highly quantitative analysis of the extremely AT-rich P. falciparum genome. Our recently published study suggests that transcription regulation by virtue of poised chromatin and differential histone modifications is unique to P. falciparum [1]. Here we describe the experiments, quality controls and chromatin immunoprecipitation-sequencing data analysis of our associated study published in Epigenetics and Chromatin [1]. Stage-specific ChIP-sequencing data for histone modifications is submitted to Gene Expression Omnibus (GEO) database under the accession number GSE63369.", "claims": [{"id": "claim-method", "statement": "Pearson correlation was calculated between the median of gene expression and histone modification for each category.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981368", "locator": "sections[12] \"Correlation of histone modifications with gene expression\" paragraph 2", "quote": "Pearson correlation was calculated between the median of gene expression and histone modification for each category."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Stage-specific ChIP-sequencing data for histone modifications is submitted to Gene Expression Omnibus (GEO) database under the accession number GSE63369.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981368", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Stage-specific ChIP-sequencing data for histone modifications is submitted to Gene Expression Omnibus (GEO) database under the accession number GSE63369."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The headline result is that histone modification profiles are predictive of gene expression. The statistical analysis used Pearson correlation between median gene expression and histone modification, and the source ChIP-sequencing data were deposited in GEO under accession GSE63369 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63369.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981368", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Histone modification profiles are predictive of gene expression"}, {"asset": "source:pmid:26981368", "locator": "sections[12] \"Correlation of histone modifications with gene expression\" paragraph 2", "quote": "Pearson correlation was calculated between the median of gene expression and histone modification for each category."}, {"asset": "source:pmid:26981368", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Stage-specific ChIP-sequencing data for histone modifications is submitted to Gene Expression Omnibus (GEO) database under the accession number GSE63369."}, {"asset": "source:pmid:26981368", "locator": "sections[3] \"p\" paragraph 1", "quote": "The direct link for the ChIP-sequencing data is -http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63369"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The headline result is that histone modification profiles are predictive of gene expression. The statistical analysis used Pearson correlation between median gene expression and histone modification, and the source ChIP-sequencing data were deposited in GEO under accession GSE63369 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63369.", "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:26981368"], "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:GSE63369"], "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:GSE63369"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26981368", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.11.026", "sha256": "sha256:8090d505ca624a4fd7ab509eb6f537bf6563af9a1d9dfbdc9ef92cf0d7080d9b", "bytes": 16222, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.11.026", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4778637", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE63369", "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=GSE63369", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63369", "version": null, "note": "Stage-specific ChIP-sequencing data for histone modifications is submitted to Gene Expression Omnibus (GEO) database under the accession number GSE63369.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Stage-specific ChIP-sequencing data for histone modifications is submitted to Gene Expression Omnibus (GEO) database under the accession number GSE63369.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1547552", "GSM1547553", "GSM1547554", "GSM1547555", "GSM1547556", "GSM1547557", "GSM1547558", "GSM1547559", "GSM1547560", "GSM1547561", "GSM1547562", "GSM1547563", "GSM1547564", "GSM1547565", "GSM1547566", "GSM1547567", "GSM1547568", "GSM1547569", "GSM1547570", "GSM1547571", "GSM1547572", "GSM1547573", "GSM1547574", "GSM1547575", "GSM1547576", "GSM1547577", "GSM1547578", "GSM1547579", "GSM1547580", "GSM1547581", "GSM1547582", "GSM1547583", "GSM1547584", "GSM1547585", "GSM1547586", "GSM1547587", "GSM1547588", "GSM1547589", "GSM1547590"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "19422", "taxon": "Plasmodium falciparum", "title": "A comprehensive epigenome map of Plasmodium falciparum reveals unique mechanisms of transcriptional regulation", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE63369 not downloaded", "asset:data:geo:GSE63369 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Pearson correlation was calculated between the median of gene expression and histone modification for each category."}}, {"id": "method-2", "family": "sequence_alignment", "specific": "read_mapping", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "bowtie"}}], "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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE63369"], "resolved_accessions": ["GSE63369"], "statements": ["Stage-specific ChIP-sequencing data for histone modifications is submitted to Gene Expression Omnibus (GEO) database under the accession number GSE63369."], "basis": "The paper names GSE63369 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": ["pearson_r"], "assets": ["source:pmid:26981368", "data:geo:GSE63369"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE63369"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:35Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 39053, "completion_tokens": 2064, "cached_tokens": 1841}}, "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:26981368", "type": "paper", "label": "pmid:26981368"}, {"id": "source:pmid:26981368", "type": "manuscript", "label": "PMID 26981368 full text"}, {"id": "data:geo:GSE63369", "type": "dataset", "label": "GEO GSE63369"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26981368", "type": "paper", "label": "pmid:26981368"}, {"id": "source:pmid:26981368", "type": "manuscript", "label": "PMID 26981368 full text"}, {"id": "data:geo:GSE63369", "type": "dataset", "label": "GEO GSE63369"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26981368", "type": "extraction", "used": ["source:pmid:26981368"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE63369", "type": "accession_resolution", "used": ["data:geo:GSE63369"], "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:26981368", "parent_hash": "sha256:02ece403838de8c24707a68125e11a1790e498f2b6d5b53c9da0327dfc05d6cd", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE63369 licence not read", "asset:data:geo:GSE63369 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": ["meric stretches as seen in P. falciparum for next-generation sequencing library amplification [2], enabling highly q"], "order_basis": "paper_text_order:842", "id": "assay:1"}, {"role": "data_generation", "definition_id": "chip_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["design, materials and methods P. falciparum ChIP-seq data processing and quality control measures", "converted to color-space using bowtie-build. ChIP-seq data were mapped using the Bowtie allowing t"], "order_basis": "paper_text_order:1540", "id": "assay:2"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Pearson correlation was calculated between the median of gene expression and histone modification for each category."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}