Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer.
Genomic technologies including microarrays and next-generation sequencing have enabled the generation of molecular signatures of prostate cancer. Lists of differentially expressed genes between malignant and non-malignant states are thought to be fertile sources of putative prostate cancer biomarker...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2015-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4687717?pdf=render |
| _version_ | 1828795128208162816 |
|---|---|
| author | Jennifer S Myers Ariana K von Lersner Charles J Robbins Qing-Xiang Amy Sang |
| author_facet | Jennifer S Myers Ariana K von Lersner Charles J Robbins Qing-Xiang Amy Sang |
| author_sort | Jennifer S Myers |
| collection | DOAJ |
| description | Genomic technologies including microarrays and next-generation sequencing have enabled the generation of molecular signatures of prostate cancer. Lists of differentially expressed genes between malignant and non-malignant states are thought to be fertile sources of putative prostate cancer biomarkers. However such lists of differentially expressed genes can be highly variable for multiple reasons. As such, looking at differential expression in the context of gene sets and pathways has been more robust. Using next-generation genome sequencing data from The Cancer Genome Atlas, differential gene expression between age- and stage- matched human prostate tumors and non-malignant samples was assessed and used to craft a pathway signature of prostate cancer. Up- and down-regulated genes were assigned to pathways composed of curated groups of related genes from multiple databases. The significance of these pathways was then evaluated according to the number of differentially expressed genes found in the pathway and their position within the pathway using Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis. The "transforming growth factor-beta signaling" and "Ran regulation of mitotic spindle formation" pathways were strongly associated with prostate cancer. Several other significant pathways confirm reported findings from microarray data that suggest actin cytoskeleton regulation, cell cycle, mitogen-activated protein kinase signaling, and calcium signaling are also altered in prostate cancer. Thus we have demonstrated feasibility of pathway analysis and identified an underexplored area (Ran) for investigation in prostate cancer pathogenesis. |
| first_indexed | 2024-12-12T03:59:01Z |
| format | Article |
| id | doaj.art-a85250602dbf40cbb202f212346abafa |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T03:59:01Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a85250602dbf40cbb202f212346abafa2022-12-22T00:39:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-011012e014532210.1371/journal.pone.0145322Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer.Jennifer S MyersAriana K von LersnerCharles J RobbinsQing-Xiang Amy SangGenomic technologies including microarrays and next-generation sequencing have enabled the generation of molecular signatures of prostate cancer. Lists of differentially expressed genes between malignant and non-malignant states are thought to be fertile sources of putative prostate cancer biomarkers. However such lists of differentially expressed genes can be highly variable for multiple reasons. As such, looking at differential expression in the context of gene sets and pathways has been more robust. Using next-generation genome sequencing data from The Cancer Genome Atlas, differential gene expression between age- and stage- matched human prostate tumors and non-malignant samples was assessed and used to craft a pathway signature of prostate cancer. Up- and down-regulated genes were assigned to pathways composed of curated groups of related genes from multiple databases. The significance of these pathways was then evaluated according to the number of differentially expressed genes found in the pathway and their position within the pathway using Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis. The "transforming growth factor-beta signaling" and "Ran regulation of mitotic spindle formation" pathways were strongly associated with prostate cancer. Several other significant pathways confirm reported findings from microarray data that suggest actin cytoskeleton regulation, cell cycle, mitogen-activated protein kinase signaling, and calcium signaling are also altered in prostate cancer. Thus we have demonstrated feasibility of pathway analysis and identified an underexplored area (Ran) for investigation in prostate cancer pathogenesis.http://europepmc.org/articles/PMC4687717?pdf=render |
| spellingShingle | Jennifer S Myers Ariana K von Lersner Charles J Robbins Qing-Xiang Amy Sang Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer. PLoS ONE |
| title | Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer. |
| title_full | Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer. |
| title_fullStr | Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer. |
| title_full_unstemmed | Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer. |
| title_short | Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer. |
| title_sort | differentially expressed genes and signature pathways of human prostate cancer |
| url | http://europepmc.org/articles/PMC4687717?pdf=render |
| work_keys_str_mv | AT jennifersmyers differentiallyexpressedgenesandsignaturepathwaysofhumanprostatecancer AT arianakvonlersner differentiallyexpressedgenesandsignaturepathwaysofhumanprostatecancer AT charlesjrobbins differentiallyexpressedgenesandsignaturepathwaysofhumanprostatecancer AT qingxiangamysang differentiallyexpressedgenesandsignaturepathwaysofhumanprostatecancer |