Gene function analysis and underlying mechanism of esophagus cancer based on microarray gene expression profiling.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29285246", "kind": "science-record", "revision": 8, "content_hash": "sha256:d44b32892e569924447f6184ca5e1d795d3a5087c7dd6ca8dbb455f765838bcc", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T21:59:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene function analysis and underlying mechanism of esophagus cancer based on microarray gene expression profiling.", "doi": "10.18632/oncotarget.22160", "pmid": "29285246", "authors": ["Ying Yue", "Mengjia Song", "Yamin Qiao", "Pupu Li", "Yiqiang Yuan", "Jingyao Lian", "Suying Wang", "Yi Zhang"], "journal": "Oncotarget", "year": 2017, "abstract": "Esophageal cancer (EC) is one of the most common digestive malignant tumors worldwide. Over the past decades, there have been minimal improvements in outcomes for patients with EC. New targets and novel therapies are needed to improve outcomes for these patients. This study aimed to explore the molecular mechanisms of EC by integrated bioinformatic analyses of the feature genes associated with EC and correlative gene functions which can distinguish cancerous tissues from non-cancerous tissues. Gene expression profile GSE20347 was downloaded from Gene Expression Omnibus (GEO) database, including 17 EC samples and their paired adjacent non-cancerous samples. The differentially expressed genes (DEGs) between EC and normal specimens were identified and then applied to analyze the GO enrichment on gene functions and KEGG pathways. Corresponding Pathway Relation Network (Pathway-net) and Gene Signal Network (signal-net) of DEGs were established based on the data collected from GCBI datasets. The results showed that DEGs mainly participated in the process of cell adhesion, cell proliferation, survival, invasion, metastasis and angiogenesis. Aberrant expression of PTK2, MAPK signaling pathway, PI3K-Akt signaling pathway, p53 signaling pathway and MET were closely associated with EC carcinogenesis. Importantly, Interleukin 8 (IL8) and C-X-C chemokine receptor type 7 (CXCR-7) were predicted to be significantly related to EC. These findings were further validated by analyzing both TCGA database and our clinical samples of EC. Our discovery provides a registry of genes and pathways that are disrupted in EC, which has the potential to be used in clinic for diagnosis and target therapy of EC in future.", "claims": [{"id": "claim-method", "statement": "Then, DEGs between EC and normal tissues were identified with the FC method (no less than 3 biological replicates each group) and the Significance Analysis of Microarrays (SAM) method (no less than3 biological replicates each group) [24].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29285246", "locator": "sections[13] \"DEGs screening and hierarchical cluster analysis\" paragraph 2", "quote": "Then, DEGs between EC and normal tissues were identified with the FC method (no less than 3 biological replicates each group) and the Significance Analysis of Microarrays (SAM) method (no less than3 biological replicates each group) [24]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression profile GSE20347 was downloaded from Gene Expression Omnibus (GEO) database, including 17 EC samples and their paired adjacent non-cancerous samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29285246", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Gene expression profile GSE20347 was downloaded from Gene Expression Omnibus (GEO) database, including 17 EC samples and their paired adjacent non-cancerous samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using fold change and the Significance Analysis of Microarrays (SAM) method with q-value-based false discovery rate control, the study analyzed GSE20347 downloaded from GEO, comprising 17 paired esophageal cancer and adjacent non-cancerous samples, and identified 1,348 differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29285246", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Gene expression profile GSE20347 was downloaded from Gene Expression Omnibus (GEO) database, including 17 EC samples and their paired adjacent non-cancerous samples."}, {"asset": "source:pmid:29285246", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The differentially expressed genes (DEGs) between EC and normal specimens were identified and then applied to analyze the GO enrichment on gene functions and KEGG pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using fold change and the Significance Analysis of Microarrays (SAM) method with q-value-based false discovery rate control, the study analyzed GSE20347 downloaded from GEO, comprising 17 paired esophageal cancer and adjacent non-cancerous samples, and identified 1,348 differentially expressed genes.", "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:29285246"], "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:GSE20347"], "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:GSE20347"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29285246", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.22160", "sha256": 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