Dataset Information

RNA-Sequence Analysis Reveals Differentially Expressed Genes (DEGs) in Patients Exhibiting Different Risks of Tumor Metastasis.

ABSTRACT: BACKGROUND Breast cancer is one of the most common malignancies in women. In a previous study, we found that for two patients who had a high risk of lymphatic metastasis, lymphatic metastasis did not occur; whereas, for two patients who had a low risk of lymphatic metastasis, lymphatic metastasis did occur. MATERIAL AND METHODS We analyzed the differential gene expressions of these four patients by RNA-sequence. The data (HRNM_T versus HRNM_N, LRYM_T versus LRYM_N, and HRNM_T versus LRYM_T) was then processed using differentially expressed genes (DEGs) analysis, functional analysis for DEGs, and PPI network construct. RESULTS For HRNM_T versus HRNM_N, there were 224 DEGs. There were 504 DEGs for LRYM_T versus LRYM_N, and 88 DEGs for LRYM_T versus LRYM_N. For HRNM_T versus HRNM_N, DEGs were up-regulated mainly in the cell cycle, the IL-17 signaling pathway, and the progesterone-mediated oocyte maturation; DEGs were down-regulated mainly in the IL-17 signaling pathway. For LRYM_T versus LRYM_N, DEGs were up-regulated mainly in protein digestion and absorption, and cytokine-cytokine receptor interaction; DEGs were down-regulated mainly in ECM-receptor interaction. For HRNM_T versus LRYM_T, DEGs were up-regulated mainly in the PPAR signaling pathway; DEGs were downregulated mainly in the adipocytokine signaling pathway. The DEGs were screened to construct PPI networks. CONCLUSIONS The GO and KEGG functional enrichments of HRNM_T versus HRNM_N, and LRYM_T versus LRYM_N were consistent with earlier studies. For HRNM_T versus LRYM_T, DEGs were up-regulated mainly in PPAR signaling; DEGs were down-regulated mainly in the adipocytokine pathway.

SUBMITTER: Dong LF

PROVIDER: S-EPMC5475372 | biostudies-other | 2017 Jun

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

RNA-Sequence Analysis Reveals Differentially Expressed Genes (DEGs) in Patients Exhibiting Different Risks of Tumor Metastasis.

Dong Li-Feng LF Xu Shu-Ying SY Long Jing-Pei JP Wan Fang F Chen Yi-Ding YD

Medical science monitor : international medical journal of experimental and clinical research 20170611

BACKGROUND Breast cancer is one of the most common malignancies in women. In a previous study, we found that for two patients who had a high risk of lymphatic metastasis, lymphatic metastasis did not occur; whereas, for two patients who had a low risk of lymphatic metastasis, lymphatic metastasis did occur. MATERIAL AND METHODS We analyzed the differential gene expressions of these four patients by RNA-sequence. The data (HRNM_T versus HRNM_N, LRYM_T versus LRYM_N, and HRNM_T versus LRYM_T) was ...[more]

PMID: 28601889

Similar Datasets

Project description:Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture. However the gene discovery in this species has been limited to small-scale data collection in China. We used the next generation sequencing technology for the experiment; the transcriptome was sequenced of samples of hepatopancreas organ in individuals from 4 GFP groups (A1, A2, B1 and B2). De novo transcriptome sequencing generated 66,953 isogenes. Using BLASTX to search the Non-redundant (NR), Search Tool for the Retrieval of Interacting Genes (STRING), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases; 21,224 unigenes were annotated, 9,552 matched unigenes with the Gene Ontology (GO) classification; 5,782 matched unigenes in 25 categories of Clusters of Orthologous Groups of proteins (COG) and 20,859 unigenes were consequently assigned to 312 KEGG pathways. Between the A and B groups 147 differentially expressed genes (DEGs) were identified; between the A1 and A2 groups 6,860 DEGs were identified and between the B1 and B2 groups 5,229 DEGs were identified. After enrichment, the A and B groups identified 38 DEGs, but none of them were significantly enriched. The A1 and A2 groups identified 21,856 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function and the KEGG pathway defined 2,459 genes had a KEGG Ortholog-ID (KO-ID) and could be categorized into 251 pathways, of those, 9 pathways were significantly enriched. The B1 and B2 groups identified 5,940 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function, and the KEGG pathway defined 1,543 genes had a KO-ID and could be categorized into 240 pathways, of those, 2 pathways were significantly enriched. We investigated 99 queries (GO) which related to growth of GFP in 4 groups. After enrichment we identified 23 DEGs and 1 KEGG PATHWAY 'ko04711' relation with GFP growth.

Dataset Information

RNA-Sequence Analysis Reveals Differentially Expressed Genes (DEGs) in Patients Exhibiting Different Risks of Tumor Metastasis.

Publications

RNA-Sequence Analysis Reveals Differentially Expressed Genes (DEGs) in Patients Exhibiting Different Risks of Tumor Metastasis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets