Data set for transcriptional response to depletion of the Shoc2 scaffolding protein.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27077079", "kind": "science-record", "revision": 6, "content_hash": "sha256:5f829534fe87377e0065baa85919f10e55c53bd00ccb4de29e2dc51c265b8739", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T21:20:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data set for transcriptional response to depletion of the Shoc2 scaffolding protein.", "doi": "10.1016/j.dib.2016.03.012", "pmid": "27077079", "authors": ["Eric C Rouchka", "Myoungkun Jeoung", "Eun Ryoung Jang", "Jinpeng Liu", "Chi Wang", "Xiaohong Li", "Emilia Galperin"], "journal": "Data in brief", "year": 2016, "abstract": "The Suppressor of Clear, Caenorhabditis elegans Homolog (SHOC2) is a scaffold protein that positively modulates activity of the RAS/ERK1/2 MAP kinase signaling cascade. We set out to understand the ERK1/2 pathway transcriptional response transduced through the SHOC2 scaffolding module. This data article describes raw gene expression within triplicates of kidney fibroblast-like Cos1 cell line expressing non-targeting shRNA (Cos-NT) and triplicates of Cos1 cells depleted of SHOC2 using shRNA (Cos-LV1) upon activation of ERK1/2 pathway by the Epidermal Growth Factor Receptor (EGFR). The data referred here is available in NCBI׳s Gene Expression Omnibus (GEO), accession GEO: GSE67063 as well as NCBI׳s Sequence Read Archive (SRA), accession SRA: SRP056324. A complete analysis of the results can be found in \"Shoc2-tranduced ERK1/2 motility signals - Novel insights from functional genomics\"(Jeoung et al., 2016) [1].", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes were identified by comparing the combined alignments of samples 4, 5 and 6 (LV1) to the combined alignments of samples 1, 2 and 3 (NT) using cuffdiff2 (version 2.1.1) [11] with the multithreading option -p 8 and the minimum alignment count of 7 (--min-alignment-count 7) to determine gene expression levels in Fragments Per Kilobase of transcript per Megabase (FPKM) and differential expression between the two conditions. A false-discovery rate (FDR) corrected q-value cutoff of 0.05 was used to determine differentially expressed genes. Data is available in the Gene Expression Omnibus (GEO) [2], [3] accession GEO: GSE637063 through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67063 as well as through NCBI׳s Sequence Read Archive [4] through the direct link http://www.ncbi.nlm.nih.gov/sra?term=SRP056324.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27077079", "locator": "sections[9] \"Data acquisition\" paragraph 6", "quote": "Differentially expressed genes were identified by comparing the combined alignments of samples 4, 5 and 6 (LV1) to the combined alignments of samples 1, 2 and 3 (NT) using cuffdiff2 (version 2.1.1) [11] with the multithreading option -p 8 and the minimum alignment count of 7 (--min-alignment-count 7) to determine gene expression levels in Fragments Per Kilobase of transcript per Megabase (FPKM) and differential expression between the two conditions."}, {"asset": "source:pmid:27077079", "locator": "sections[9] \"Data acquisition\" paragraph 6", "quote": "A false-discovery rate (FDR) corrected q-value cutoff of 0.05 was used to determine differentially expressed genes."}, {"asset": "source:pmid:27077079", "locator": "sections[5] \"Data\" paragraph 2", "quote": "Data is available in the Gene Expression Omnibus (GEO) [2], [3] accession GEO: GSE637063 through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67063 as well as through NCBI׳s Sequence Read Archive [4] through the direct link http://www.ncbi.nlm.nih.gov/sra?term=SRP056324."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data referred here is available in NCBI׳s Gene Expression Omnibus (GEO), accession GEO: GSE67063 as well as NCBI׳s Sequence Read Archive (SRA), accession SRA: SRP056324.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27077079", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data referred here is available in NCBI׳s Gene Expression Omnibus (GEO), accession GEO: GSE67063 as well as NCBI׳s Sequence Read Archive (SRA), accession SRA: SRP056324."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:27077079"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27077079", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.03.012", "sha256": 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(GO:0016247)", "1", "0.10"], ["Antioxidant activity (GO:0016209)", "1", "0.10"]], "row_count": 12, "column_count": 3, "numeric_cells": 33, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t0050"}}, {"id": "asset:table:pmid:27077079:11", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:57635f9113027cf550a445344ae58e266b5a7714070bad4c1983db62b5cc716b", "bytes": 642, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#t0055", "version": null, "note": "Gene Ontology Cellular Component (GO:CC) enriched categories determined by Panther.", "structure": {"pmcid": "PMC4816878", "section_index": 11, "section_title": "Categorical enrichment", "row_count": 9, "column_count": 3}, "table": {"label": "Table 11", "caption": "Gene Ontology Cellular Component (GO:CC) enriched categories determined by Panther.", "rows": [["GO Cellular Component", "# of genes", "Percentage (%)"], ["Cell part (GO:0044464)", "130", "36.00"], ["Organelle (GO:0043226)", "74", "20.50"], ["Membrane (GO:0016020)", "53", "14.70"], ["Extracellular region (GO:0005576)", "48", "13.30"], ["Extracellular matrix (GO:0031012)", "26", "7.20"], ["Macromolecular complex (GO:0032991)", "22", "6.10"], ["Synapse (GO:0045202)", "4", "1.10"], ["Cell junction (GO:0030054)", "4", "1.10"]], "row_count": 9, "column_count": 3, "numeric_cells": 24, "header_rows": 1, "locator": "section[11]/table-wrap[2]#t0055"}}, {"id": "asset:table:pmid:27077079:12", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:12a60223e5a0ce26b37f2954d80a669c8bebc665bc4aab0488b346aa5dd4e4fe", "bytes": 1463, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[3]#t0060", "version": null, "note": "Panther Protein Class enriched categories.", "structure": {"pmcid": "PMC4816878", "section_index": 11, "section_title": "Categorical enrichment", "row_count": 29, "column_count": 3}, "table": {"label": "Table 12", "caption": "Panther Protein Class enriched categories.", "rows": [["Panther Protein Class", "# of Genes", "Percentage (%)"], ["Nucleic acid binding (PC00171)", "102", "11.30"], ["Transcription factor (PC00218)", "98", "10.80"], ["Receptor (PC00197)", "92", "10.20"], ["Hydrolase (PC00121)", "72", "7.90"], ["Transferase (PC00220)", "67", "7.40"], ["Signaling molecule (PC00207)", "63", "7.00"], ["Transporter (PC00227)", "53", "5.80"], ["Enzyme modulator (PC00095)", "53", "5.80"], ["Cytoskeletal protein (PC00085)", "34", "3.80"], ["Oxidoreductase (PC00176)", "34", "3.80"], ["Kinase (PC00137)", "29", "3.20"], ["Protease (PC00190)", "28", "3.10"], ["Extracellular matrix protein (PC00102)", "27", "3.00"], ["Cell adhesion molecule (PC00069)", "22", "2.40"], ["Defense/immunity protein (PC00090)", "19", "2.10"], ["Transfer/carrier protein (PC00219)", "18", "2.00"], ["Membrane traffic protein (PC00150)", "18", "2.00"], ["Calcium-binding protein (PC00060)", "17", "1.90"], ["Phosphatase (PC00181)", "11", "1.20"], ["Ligase (PC00142)", "10", "1.10"], ["Structural protein (PC00211)", "10", "1.10"], ["Cell junction protein (PC00070)", "8", "0.90"], ["Transmembrane receptor regulatory/adaptor protein (PC00226)", "6", "0.70"], ["Lyase (PC00144)", "6", "0.70"], ["Surfactant (PC00212)", "4", "0.40"], ["Chaperone (PC00072)", "3", "0.30"], ["Storage protein (PC00210)", "1", "0.10"], ["Isomerase (PC00135)", "1", "0.10"]], "row_count": 29, "column_count": 3, "numeric_cells": 84, "header_rows": 1, "locator": "section[11]/table-wrap[3]#t0060"}}, {"id": "asset:table:pmid:27077079:13", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c8d33ab0c3d98c32746b5db73587ea98f15fc14aa5f55b8fc65d55b7cd7da5a4", "bytes": 994, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[4]#t0065", "version": null, "note": "Gene Ontology Biological Process (GO:BP) enriched categories determined by Panther.", "structure": {"pmcid": "PMC4816878", "section_index": 11, "section_title": "Categorical enrichment", "row_count": 15, "column_count": 3}, "table": {"label": "Table 13", "caption": "Gene Ontology Biological Process (GO:BP) enriched categories determined by Panther.", "rows": [["Panther Biological Process", "# of genes", "Percentage (%)"], ["Metabolic process (GO:0008152)", "351", "22.00"], ["Cellular process (GO:0009987)", "324", "20.30"], ["Biological regulation (GO:0065007)", "210", "13.10"], ["Developmental process (GO:0032502)", "166", "10.40"], ["Localization (GO:0051179)", "125", "7.80"], ["Multicellular organismal process (GO:0032501)", "109", "6.80"], ["Response to stimulus (GO:0050896)", "93", "5.80"], ["Immune system process (GO:0002376)", "75", "4.70"], ["Cellular component 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A false-discovery rate (FDR) corrected q-value cutoff of 0.05 was used to determine differentially expressed genes. Data is available in the Gene Expression Omnibus (GEO) [2], [3] accession GEO: GSE637063 through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67063 as well as through NCBI׳s Sequence Read Archive [4] through the direct link http://www.ncbi.nlm.nih.gov/sra?term=SRP056324."}}], "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (cuffdiff2 differential expression analysis using an FDR-corrected q-value cutoff of 0.05; source data are available through GEO accession GSE67063 and SRA accession SRP056324), 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. 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