About: Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach

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About: Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach
Creator	Lee, Yun-Shien Hsieh, Sen-Yung Lee, Wei-Chen Lee, Yung-Lin Pan, Yi-Shin
Source	PMC
abstract	BACKGROUND: The main limitation in performing genome-wide gene-expression profiling is the assay of low-expression genes. Approaches with high throughput and high sensitivity for assaying low-expression transcripts are urgently needed for functional genomic studies. Combination of the suppressive subtractive hybridization (SSH) and cDNA microarray techniques using the subtracted cDNA clones as probes printed on chips has greatly improved the efficiency for fishing out the differentially expressed clones and has been used before. However, it remains tedious and inefficient sequencing works for identifying genes including the great number of redundancy in the subtracted amplicons, and sacrifices the original advantages of high sensitivity of SSH in profiling low-expression transcriptomes. RESULTS: We modified the previous combination of SSH and microarray methods by directly using the subtracted amplicons as targets to hybridize the pre-made cDNA microarrays (named as %22SSH/microarray%22). mRNA prepared from three pairs of hepatoma and non-hepatoma liver tissues was subjected to the SSH/microarray assays, as well as directly to regular cDNA microarray assays for comparison. As compared to the original SSH and microarray combination assays, the modified SSH/microarray assays allowed for much easier inspection of the subtraction efficiency and identification of genes in the subtracted amplicons without tedious and inefficient sequencing work. On the other hand, 5015 of the 9376 genes originally filtered out by the regular cDNA microarray assays because of low expression became analyzable by the SSH/microarray assays. Moreover, the SSH/microarray assays detected about ten times more (701 vs. 69) HCC differentially expressed genes (at least a two-fold difference and P < 0.01), particularly for those with rare transcripts, than did the regular cDNA microarray assays. The differential expression was validated in 9 randomly selected genes in 18 pairs of hepatoma/non-hepatoma liver tissues using quantitative RT-PCR. The SSH/microarray approaches resulted in identifying many differentially expressed genes implicated in the regulation of cell cycle, cell death, signal transduction and cell morphogenesis, suggesting the involvement of multi-biological processes in hepato-carcinogenesis. CONCLUSION: The modified SSH/microarray approach is a simple but high-sensitive and high-efficient tool for differentially profiling the low-expression transcriptomes. It is most adequate for applying to functional genomic studies.
has issue date	2006-05-31(xsd:dateTime)
bibo:doi	10.1186/1471-2164-7-131
bibo:pmid	16737534
has license	cc-by
sha1sum (hex)	4db3931c4b24ae432d68b7e24f593b1272445523
schema:url	https://doi.org/10.1186/1471-2164-7-131
resource representing a document's title	Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach
has PubMed Central identifier	PMC1522022
has PubMed identifier	16737534
schema:publication	BMC Genomics
resource representing a document's body	covid:4db3931c4b24ae432d68b7e24f593b1272445523#body_text
is schema:about of	named entity 'EXPRESSION' named entity 'APPROACH' named entity 'sensitivity' named entity 'genes' named entity 'genomic' named entity 'throughput' named entity 'sequencing' named entity 'GENOMICS' named entity 'SSH' named entity 'CLONES' named entity 'TRANSCRIPTS' named entity 'IMPROVED' named entity 'SACRIFICES' named entity 'GENES' named entity 'GENOME' named entity 'WIDE' named entity 'HIGH THROUGHPUT' named entity 'REDUNDANCY' named entity 'EXPRESSION PROFILING' named entity 'PRINTED' named entity 'WORKS' named entity 'EFFICIENCY' named entity 'EXPRESSION' named entity 'SUPPRESSIVE' named entity 'STUDIES' named entity 'ORIGINAL' named entity 'USING' named entity 'INCLUDING' named entity 'ASSAY' named entity 'FUNCTIONAL GENOMIC' named entity 'SSH' named entity 'GREATLY' named entity 'FISHING' named entity 'PERFORMING' named entity 'LOW' named entity 'TECHNIQUES' named entity 'SUBTRACTIVE HYBRIDIZATION' named entity 'HUMAN' named entity 'USING' named entity 'NOVEL' named entity 'HEPATOMA' named entity 'LIMITATION' named entity 'PROBES' named entity 'IDENTIFYING' named entity 'APPROACHES' named entity 'CDNA' named entity 'NEEDED' named entity 'INEFFICIENT' named entity 'CDNA MICROARRAY' named entity 'GREAT' named entity 'HIGH SENSITIVITY' named entity 'BMC' named entity 'USED' named entity 'NUMBER OF' named entity 'LOW' named entity 'SEQUENCING' named entity 'EXPRESSED' named entity 'CHIPS' named entity 'COMBINATION' named entity 'MAIN' named entity 'GENE-EXPRESSION' covid:arg/4db3931c4b24ae432d68b7e24f593b1272445523 named entity 'REMAINS' named entity 'subtracted' named entity 'needed' named entity 'cDNA clones' named entity 'SSH' named entity 'advantages' named entity 'transcriptomes' named entity 'improved' named entity 'profiling' named entity 'human' named entity 'differentially expressed' named entity 'expression profiling' named entity 'hepatoma' named entity 'expressed' named entity 'VLDLR'

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