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A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale in silico analysis.

Benbow L, Wang L, Laverty M, Liu S, Qiu P, Bond RW, Gustafson E, Hedrick JA, Kostich M, Greene JR, Wang L - BMC Genomics (2002)

Bottom Line: 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.This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Discovery Technology Department, Schering-Plough Research Institute, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA. lawrence.benbow@spcorp.com

ABSTRACT

Background: The EST database provides a rich resource for gene discovery and in silico expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to IL-8.

Results: 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.

Conclusions: This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes.

No MeSH data available.


Related in: MedlinePlus

Distribution of IL-8 related genes in tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/IL-8 clones (Rtumor) was calculated for each IL-8 related gene. The result is plotted here with gene id on the x-axis and Rtumor on the y-axis. A bimodal distribution is obtained where most genes are either highly associated (>80%) with tumor libraries or they show very little association (<10%) with tumor libraries. Five genes have an Rtumor value of >95%: KLF2 (99.5%), PS1 (98.9%), NPDC1 (97.9%), GW112 protein (97.4%), and claudin-3 (96.6%).
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Figure 1: Distribution of IL-8 related genes in tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/IL-8 clones (Rtumor) was calculated for each IL-8 related gene. The result is plotted here with gene id on the x-axis and Rtumor on the y-axis. A bimodal distribution is obtained where most genes are either highly associated (>80%) with tumor libraries or they show very little association (<10%) with tumor libraries. Five genes have an Rtumor value of >95%: KLF2 (99.5%), PS1 (98.9%), NPDC1 (97.9%), GW112 protein (97.4%), and claudin-3 (96.6%).

Mentions: The significance of this study lies in the generation of a complete reference database for IL-8 co-expressed genes. We present here a list of 36 genes with high EST clone count (>= 100) and high Z-score (>= 3) (referred to as IL-8 genes, I-1, I-2, ..., I-36) (Table 4) to illustrate the usage of this reference database. A high EST clone count is used to ensure the statistic significance of the data mining results. IL-8 tissues represent both tumor tissues/cells (IL-8-tumor) and non-tumor tissues/cells (Table 1 and Additional file 1). To generate a tumor expression profile, the percentage of IL-8-tumor clones versus IL-8 clones (Rtumor) was calculated for the 36 IL-8 genes. The resulting graph is shown in Figure 1. The Rtumor profile reveals a bimodal distribution. In the case of IL-8, tumor clones account for approximately 17% of all IL-8 clones (Rtumor = 17%). Eleven IL-8 genes exhibit a Rtumor of greater than 80%; five of these being greater than 95% (kruppel-like factor 2 (KLF2), presenilin 1 (PS1), neural proliferation and differentiation control protein-1 (NPDC1), GW112 and claudin-3). On the other hand, eight genes were not found in any IL-8-tumor related library (Rtumor = 0).


A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale in silico analysis.

Benbow L, Wang L, Laverty M, Liu S, Qiu P, Bond RW, Gustafson E, Hedrick JA, Kostich M, Greene JR, Wang L - BMC Genomics (2002)

Distribution of IL-8 related genes in tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/IL-8 clones (Rtumor) was calculated for each IL-8 related gene. The result is plotted here with gene id on the x-axis and Rtumor on the y-axis. A bimodal distribution is obtained where most genes are either highly associated (>80%) with tumor libraries or they show very little association (<10%) with tumor libraries. Five genes have an Rtumor value of >95%: KLF2 (99.5%), PS1 (98.9%), NPDC1 (97.9%), GW112 protein (97.4%), and claudin-3 (96.6%).
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC131052&req=5

Figure 1: Distribution of IL-8 related genes in tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/IL-8 clones (Rtumor) was calculated for each IL-8 related gene. The result is plotted here with gene id on the x-axis and Rtumor on the y-axis. A bimodal distribution is obtained where most genes are either highly associated (>80%) with tumor libraries or they show very little association (<10%) with tumor libraries. Five genes have an Rtumor value of >95%: KLF2 (99.5%), PS1 (98.9%), NPDC1 (97.9%), GW112 protein (97.4%), and claudin-3 (96.6%).
Mentions: The significance of this study lies in the generation of a complete reference database for IL-8 co-expressed genes. We present here a list of 36 genes with high EST clone count (>= 100) and high Z-score (>= 3) (referred to as IL-8 genes, I-1, I-2, ..., I-36) (Table 4) to illustrate the usage of this reference database. A high EST clone count is used to ensure the statistic significance of the data mining results. IL-8 tissues represent both tumor tissues/cells (IL-8-tumor) and non-tumor tissues/cells (Table 1 and Additional file 1). To generate a tumor expression profile, the percentage of IL-8-tumor clones versus IL-8 clones (Rtumor) was calculated for the 36 IL-8 genes. The resulting graph is shown in Figure 1. The Rtumor profile reveals a bimodal distribution. In the case of IL-8, tumor clones account for approximately 17% of all IL-8 clones (Rtumor = 17%). Eleven IL-8 genes exhibit a Rtumor of greater than 80%; five of these being greater than 95% (kruppel-like factor 2 (KLF2), presenilin 1 (PS1), neural proliferation and differentiation control protein-1 (NPDC1), GW112 and claudin-3). On the other hand, eight genes were not found in any IL-8-tumor related library (Rtumor = 0).

Bottom Line: 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.This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Discovery Technology Department, Schering-Plough Research Institute, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA. lawrence.benbow@spcorp.com

ABSTRACT

Background: The EST database provides a rich resource for gene discovery and in silico expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to IL-8.

Results: 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.

Conclusions: This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes.

No MeSH data available.


Related in: MedlinePlus