Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human prostate tissues obtained from multiple Institutions

ABSTRACT: Microarray studies of Prostate tissues obtained from multiple Institutions. Analysis done during Aug. 2002 to June 2004.

ORGANISM(S): Homo sapiens

DISEASE(S): prostate cancer

SUBMITTER: Carlos Moreno

PROVIDER: E-TABM-26 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Sex-determining region Y box 4 is a transforming oncogene in human prostate cancer cells.

Liu Pengbo P Ramachandran Sumathi S Ali Seyed Mohamed M Scharer Christopher D CD Laycock Noelani N Dalton W Brian WB Williams Holly H Karanam Suresh S Datta Milton W MW Jaye David L DL Moreno Carlos S CS

Cancer research 20060401 8

Prostate cancer is the most commonly diagnosed noncutaneous neoplasm and second most common cause of cancer-related mortality in western men. To investigate the mechanisms of prostate cancer development and progression, we did expression profiling of human prostate cancer and benign tissues. We show that the SOX4 is overexpressed in prostate tumor samples compared with benign tissues by microarray analysis, real-time PCR, and immunohistochemistry. We also show that SOX4 expression is highly corr ...[more]

PMID: 16618720

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Project description:Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by wide-spread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts. In order to transfer genetic information encoded in the genomic sequence of an organism into functional features, the genomic sequence must be transcribed. According to the current genome annotation, the human genome produces transcripts from 20,00025,000 protein-coding genes and a smaller number of non-coding genes. Recently, the introduction of tiling arrays that enable the measurement of transcription regardless of previous annotation challenged this view by providing evidence that a large proportion of transcription occurs outside of annotated genes. It has been suggested that these transcripts represent previously unidentified functional RNAs as well as extensions of known genes. However, their lack of conservation between species on the DNA sequence level raises questions about their functionality. In this study we assess the functionality of these novel transcripts by testing the extent to which their expression is conserved between humans and chimpanzees in different tissues. Surprisingly, we find the expression of known and novel transcripts to be conserved to the same relative extent when different tissues are compared. This suggests that both known and novel transcripts are equally affected by adaptive and stabilizing selection in different tissues during human and chimpanzee evolution. Further, in terms of absolute numbers, about half of the expression differences between humans and chimpanzees in any given tissue are due to intergenic transcripts.

Dataset Information

Transcription profiling of human prostate tissues obtained from multiple Institutions

Publications

Sex-determining region Y box 4 is a transforming oncogene in human prostate cancer cells.

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