Co-expression Network Analysis of Biomarkers for Adrenocortical Carcinoma.

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We firstly used the microarray data from public database Gene Expression Omnibus database to construct a weighted gene co-expression network, and then to identify gene modules associated with clinical features of ACC. Though this algorithm, a significant module with R2 = 0.64 (P = 9 × 10-5) was identified. Co-expression network and protein-protein interaction network were performed for screen the candidate hub genes. Checked by The Cancer Genome Atlas (TCGA) database, another independent dataset GSE19750, and GEPIA database, using one-way ANOVA, Pearson's correlation, survival analysis, diagnostic capacity (ROC curve) and expression level revalidation, a total 12 real hub genes were identified. Gene ontology and KEGG pathway analysis of genes in the significant module revealed that the hub genes are significantly enriched in cell cycle regulation. Moreover, gene set enrichment analysis suggests that the samples with highly expressed hub genes are correlated with cell cycle. Taken together, our integrated analysis has identified 12 hub genes that are associated with the progression and prognosis of ACC; these hub genes might lead to poor outcomes by regulating the cell cycle.", "claims": [{"id": "claim-data-access", "statement": "Dataset GSE10927 (Giordano et al., 2009) performed on Affymetrix Human Genome U133 Plus 2.0 Array was used as a training set to construct co-expression networks and identify hub genes in this study. This dataset included human samples of 33 ACCs, 22 adrenocortical adenomas, and 10 normal adrenal cortex samples, each from a different patient.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30158955", "locator": "sections[3] \"Data Collection\" paragraph 2", "quote": "Dataset GSE10927 (Giordano et al., 2009) performed on Affymetrix Human Genome U133 Plus 2.0 Array was used as a training set to construct co-expression networks and identify hub genes in this study. This dataset included human samples of 33 ACCs, 22 adrenocortical adenomas, and 10 normal adrenal cortex samples, each from a different patient."}], "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:30158955"], "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. 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