A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis
<p>Abstract</p> <p>Background</p> <p>The EST database provides a rich resource for gene discovery and <it>in silico</it> expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to I...
Main Authors: | , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2002-10-01
|
Series: | BMC Genomics |
Online Access: | http://www.biomedcentral.com/1471-2164/3/29 |
id |
doaj-dcfb10a45e0d48379f21294bb3e3eb47 |
---|---|
record_format |
Article |
spelling |
doaj-dcfb10a45e0d48379f21294bb3e3eb472020-11-25T00:51:32ZengBMCBMC Genomics1471-21642002-10-01312910.1186/1471-2164-3-29A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysisKostich MitchellHedrick Joseph AGustafson EricBond Richard WQiu PingLiu SuxingLaverty MaureenWang LynnBenbow LawrenceGreene Jonathan RWang Luquan<p>Abstract</p> <p>Background</p> <p>The EST database provides a rich resource for gene discovery and <it>in silico</it> expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to IL-8.</p> <p>Results</p> <p>IL-8 is represented in 53 dbEST cDNA libraries. We calculated the frequency of occurrence of all the genes represented in these cDNA libraries, and ranked the candidates based on a Z-score. Additional analysis suggests that most IL-8 related genes are differentially expressed between non-tumor and tumor tissues. To focus on IL-8's function in tumor tissues, we further analyzed and ranked the genes in 16 IL-8 related tumor libraries.</p> <p>Conclusions</p> <p>This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes.</p> http://www.biomedcentral.com/1471-2164/3/29 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kostich Mitchell Hedrick Joseph A Gustafson Eric Bond Richard W Qiu Ping Liu Suxing Laverty Maureen Wang Lynn Benbow Lawrence Greene Jonathan R Wang Luquan |
spellingShingle |
Kostich Mitchell Hedrick Joseph A Gustafson Eric Bond Richard W Qiu Ping Liu Suxing Laverty Maureen Wang Lynn Benbow Lawrence Greene Jonathan R Wang Luquan A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis BMC Genomics |
author_facet |
Kostich Mitchell Hedrick Joseph A Gustafson Eric Bond Richard W Qiu Ping Liu Suxing Laverty Maureen Wang Lynn Benbow Lawrence Greene Jonathan R Wang Luquan |
author_sort |
Kostich Mitchell |
title |
A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis |
title_short |
A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis |
title_full |
A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis |
title_fullStr |
A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis |
title_full_unstemmed |
A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis |
title_sort |
reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale <it>in silico</it> analysis |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2002-10-01 |
description |
<p>Abstract</p> <p>Background</p> <p>The EST database provides a rich resource for gene discovery and <it>in silico</it> expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to IL-8.</p> <p>Results</p> <p>IL-8 is represented in 53 dbEST cDNA libraries. We calculated the frequency of occurrence of all the genes represented in these cDNA libraries, and ranked the candidates based on a Z-score. Additional analysis suggests that most IL-8 related genes are differentially expressed between non-tumor and tumor tissues. To focus on IL-8's function in tumor tissues, we further analyzed and ranked the genes in 16 IL-8 related tumor libraries.</p> <p>Conclusions</p> <p>This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes.</p> |
url |
http://www.biomedcentral.com/1471-2164/3/29 |
work_keys_str_mv |
AT kostichmitchell areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT hedrickjosepha areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT gustafsoneric areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT bondrichardw areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT qiuping areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT liusuxing areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT lavertymaureen areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT wanglynn areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT benbowlawrence areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT greenejonathanr areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT wangluquan areferencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT kostichmitchell referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT hedrickjosepha referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT gustafsoneric referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT bondrichardw referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT qiuping referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT liusuxing referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT lavertymaureen referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT wanglynn referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT benbowlawrence referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT greenejonathanr referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis AT wangluquan referencedatabasefortumorrelatedgenescoexpressedwithinterleukin8usinggenomescaleitinsilicoitanalysis |
_version_ |
1725245297797365760 |