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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-tumor related genes in all tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/tumor clones (Ril8tumor) was calculated for IL-8-tumor related genes. The result is plotted here with gene id on the x-axis and Ril8tumor on the y-axis, and is ordered by decreasing Ril8tumor. Only the top half genes (21) with relatively high Ril8tumor are displayed. The 3 most specific genes are GW112 protein (86.2%), PS1 (81.1%), and KLF2 (76.4%).
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Figure 2: Distribution of IL-8-tumor related genes in all tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/tumor clones (Ril8tumor) was calculated for IL-8-tumor related genes. The result is plotted here with gene id on the x-axis and Ril8tumor on the y-axis, and is ordered by decreasing Ril8tumor. Only the top half genes (21) with relatively high Ril8tumor are displayed. The 3 most specific genes are GW112 protein (86.2%), PS1 (81.1%), and KLF2 (76.4%).

Mentions: A set of tumor cDNA libraries in which IL-8 is expressed (a subset of the IL-8 tissue cDNA libraries), was generated and is referred to as IL-8-tumor tissue. This virtual tissue consists of 16 cDNA libraries (171,521 cDNA clones) (Table 1 and Additional file 1). An IL-8-tumor gene database was established based on these libraries. The complete list of genes is provided in additional file 3, along with a distribution table based on contig size and Z-score (Table 2). We present here 42 candidate genes with relatively high levels of expression in IL-8-tumor tissue (EST clone count >= 100 and IL-8-tumor Z-score >= 3) (referred to as IL-8-tumor genes, IT-1, IT-2, ..., IT-42) (Table 5). To determine whether these genes are specifically related to IL-8-tumor tissue or whether they are also commonly found in tumors lacking IL-8 expression, the ratio between IL-8-tumor clones and general tumor clones (Ril8tumor) was plotted for IL-8-tumor genes (Figure 2). The Ril8tumor for all IL-8 tumor genes are greater than 38%, which is much higher than the expected background ratio between IL-8-tumor clones (171521, Table 1) and general tumor clones (864428, Table 1). A few of these genes are highly specific to IL-8-tumor tissues. Most notably GW 112, PS1, and KLF2 show Ril8tumor values of 86%, 81% and 76% respectively.


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-tumor related genes in all tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/tumor clones (Ril8tumor) was calculated for IL-8-tumor related genes. The result is plotted here with gene id on the x-axis and Ril8tumor on the y-axis, and is ordered by decreasing Ril8tumor. Only the top half genes (21) with relatively high Ril8tumor are displayed. The 3 most specific genes are GW112 protein (86.2%), PS1 (81.1%), and KLF2 (76.4%).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC131052&req=5

Figure 2: Distribution of IL-8-tumor related genes in all tumor cDNA libraries. The percentage ratio of IL-8-tumor clones/tumor clones (Ril8tumor) was calculated for IL-8-tumor related genes. The result is plotted here with gene id on the x-axis and Ril8tumor on the y-axis, and is ordered by decreasing Ril8tumor. Only the top half genes (21) with relatively high Ril8tumor are displayed. The 3 most specific genes are GW112 protein (86.2%), PS1 (81.1%), and KLF2 (76.4%).
Mentions: A set of tumor cDNA libraries in which IL-8 is expressed (a subset of the IL-8 tissue cDNA libraries), was generated and is referred to as IL-8-tumor tissue. This virtual tissue consists of 16 cDNA libraries (171,521 cDNA clones) (Table 1 and Additional file 1). An IL-8-tumor gene database was established based on these libraries. The complete list of genes is provided in additional file 3, along with a distribution table based on contig size and Z-score (Table 2). We present here 42 candidate genes with relatively high levels of expression in IL-8-tumor tissue (EST clone count >= 100 and IL-8-tumor Z-score >= 3) (referred to as IL-8-tumor genes, IT-1, IT-2, ..., IT-42) (Table 5). To determine whether these genes are specifically related to IL-8-tumor tissue or whether they are also commonly found in tumors lacking IL-8 expression, the ratio between IL-8-tumor clones and general tumor clones (Ril8tumor) was plotted for IL-8-tumor genes (Figure 2). The Ril8tumor for all IL-8 tumor genes are greater than 38%, which is much higher than the expected background ratio between IL-8-tumor clones (171521, Table 1) and general tumor clones (864428, Table 1). A few of these genes are highly specific to IL-8-tumor tissues. Most notably GW 112, PS1, and KLF2 show Ril8tumor values of 86%, 81% and 76% respectively.

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