Computational analysis of mRNA expression profiles identifies the ITG family and PIK3R3 as crucial genes for regulating triple negative breast cancer cell migration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24982892", "kind": "science-record", "revision": 5, "content_hash": "sha256:e893207ec791a67e228a75a20c4bfa5945b7295f088139ee9191deadb2969b34", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T21:19:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Computational analysis of mRNA expression profiles identifies the ITG family and PIK3R3 as crucial genes for regulating triple negative breast cancer cell migration.", "doi": "10.1155/2014/536591", "pmid": "24982892", "authors": ["Sukhontip Klahan", "Mei-Shin Wu", "Edward Hsi", "Chi-Cheng Huang", "Ming-Feng Hou", "Wei-Chiao Chang"], "journal": "BioMed research international", "year": 2014, "abstract": "Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer that does not express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor (Her2/neu). TNBC has worse clinical outcomes than other breast cancer subtypes. However, the key molecules and mechanisms of TNBC migration remain unclear. In this study, we compared two normalized microarray datasets from GEO database between Asian (GSE33926) and non-Asian populations (GSE46581) to determine the molecules and common pathways in TNBC migration. We demonstrated that 16 genes in non-Asian samples and 9 genes in Asian samples are related to TNBC migration. In addition, our analytic results showed that 4 genes, PIK3R3, ITGB1, ITGAL, and ITGA6, were involved in the regulation of actin cytoskeleton. Our results indicated potential genes that link to TNBC migration. This study may help identify novel therapeutic targets for drug development in cancer therapy.", "claims": [{"id": "claim-method", "statement": "Gene expression profile calculations were conducted using SAM method [22] and R (vers. 2.15.1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24982892", "locator": "sections[5] \"2.3. Gene Expression Calculations\" paragraph 2", "quote": "Gene expression profile calculations were conducted using SAM method [22] and R (vers. 2.15.1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "These two datasets were deposited in the GEO database under the respective codes GSE46581 and GSE33926. Data of GSE46581 were generated by Illumina HumanRef-8 WG-DASL v3.0 (GPL8432), a Whole-Genome DASL Assay which simultaneously analyzes over 24,000 genes with high sensitivity [19].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24982892", "locator": "sections[3] \"2.1. 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Data of GSE46581 were generated by Illumina HumanRef-8 WG-DASL v3.0 (GPL8432), a Whole-Genome DASL Assay which simultaneously analyzes over 24,000 genes with high sensitivity [19]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using Significance Analysis of Microarrays on two normalized GEO microarray datasets, the study identified 16 migration-related genes in non-Asian TNBC samples and 9 in Asian samples.", "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:24982892"], "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:GSE33926"], "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:GSE33926"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24982892", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2014/536591", "sha256": "sha256:05c0d65e59362b719d4c5bfe7b4cb9727fc3b56b1892d04d0dc4c781e4fa94ab", "bytes": 28903, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2014/536591", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4032728", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33926", "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=GSE33926", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33926", "version": null, "note": "These two datasets were deposited in the GEO database under the respective codes GSE46581 and GSE33926. 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Pathway Analysis of TNBC from Non-Asian and Asian Patients", "row_count": 9, "column_count": 3}, "table": {"label": "Table 5", "caption": "Migration related gene network in Asian and non-Asian populations.", "rows": [["", "Network", "Genes"], ["GSE46581", "Inflammatory response, cell signaling, cellular movement", "CCL21"], ["Cell death and survival, developmental disorders, skeletal and muscular disorders", "ITGA6, CCL3, ITGAX"], ["Cellular movement, cancer, tissue development", "ITGB1, ITGAL, CD226"], [""], ["GSE33926", "Dermatological diseases and conditions, cellular development, cellular growth and proliferation", "MIA, PIK3R3"], ["Organ morphology, reproductive system development and function, developmental disorders", "AR, CCR7"], ["Cell cycle, DNA replication, recombination, and repair, cellular assembly and organization", "CDKN2A, EN1, PITX2"], ["Cellular development, cellular growth and proliferation, tumor morphology", "TFPI"]], "row_count": 9, "column_count": 3, "numeric_cells": 4, "header_rows": 1, "locator": "section[11]/table-wrap[2]#tab5"}}, {"id": "asset:table:pmid:24982892:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e1819e7c33000803b42f97c4bcbbb4fc2925e6332d28a2b2afb4d4eceff0d083", "bytes": 568, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[3]#tab6", "version": null, "note": "Migration related canonical pathway in Asian and non-Asian populations.", "structure": {"pmcid": "PMC4032728", "section_index": 11, "section_title": "3.3. 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