Interaction of key pathways in sorafenib-treated hepatocellular carcinoma based on a PCR-array.

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The gene expression profile of GSE33621, including 6 sorafenib treated group and 6 control samples, was downloaded from the GEO (Gene Expression Omnibus) database. The differentially expressed genes (DEGs) in HCC samples were screened using the ΔΔCt method with the homogenized internal GAPDH. Also, the functions and pathways of DEGs were analyzed using the DAVID. Moreover, the significant pathways of DEGs that involved in HCC were analyzed based on the Latent pathway identification analysis (LPIA). A total of 44 down-regulated DEGs were selected in HCC samples. Also, there were 84 biological pathways that these 44 DEGs involved in. Also, LPIA showed that Osteoclast differentiation and hsa04664-Fc epsilon RI signaling pathway was the most significant interaction pathways. Moreover, Apoptosis, Toll-like receptor signaling pathway, Chagas disease, and T cell receptor signaling pathway were the significant pathways that interacted with hsa04664. In addition, DEGs such as AKT1 (v-akt murine thymoma viral oncogene homolog 1), TNF (tumor necrosis factor), SYK (spleen tyrosine kinase), and PIK3R1 (phosphoinositide-3-kinase, regulatory subunit 1 (alpha)) were the common genes that involved in the significant pathways. Several pathway interaction pairs that caused by several downregulated genes such as SYK, PI3K, AKT1, and TNF, were identified play curial role in sorafenib treated HCC. Sorafenib played important inhibition roles in HCC by affecting a complicate pathway interaction network.", "claims": [{"id": "claim-target-result", "statement": "Using the ΔΔCt method on GSE33621 gene-expression data downloaded from GEO, the study identified 44 down-regulated DEGs involved in 84 biological pathways, with LPIA identifying Osteoclast differentiation and hsa04664-Fc epsilon RI signaling pathway as the most significant interaction pathways.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26045814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene expression profile of GSE33621, including 6 sorafenib treated group and 6 control samples, was downloaded from the GEO (Gene Expression Omnibus) database."}, {"asset": "source:pmid:26045814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The differentially expressed genes (DEGs) in HCC samples were screened using the ΔΔCt method with the homogenized internal GAPDH."}, {"asset": "source:pmid:26045814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 44 down-regulated DEGs were selected in HCC samples."}, {"asset": "source:pmid:26045814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Also, there were 84 biological pathways that these 44 DEGs involved in."}, {"asset": "source:pmid:26045814", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Also, LPIA showed that Osteoclast differentiation and hsa04664-Fc epsilon RI signaling pathway was the most significant interaction pathways."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "partial", "objective": "Using the ΔΔCt method on GSE33621 gene-expression data downloaded from GEO, the study identified 44 down-regulated DEGs involved in 84 biological pathways, with LPIA identifying Osteoclast differentiation and hsa04664-Fc epsilon RI signaling pathway as the most significant interaction pathways.", "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:26045814"], "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. 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