ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
Example 1. Gene Expression in Ovarian Cancer Reflects Both Morphology and Biological Behavior, Distinguishing Clear Cell from Other Poor-Prognosis Ovarian Carcinomas
Gene expression in 113 ovarian epithelial tumors using oligonucleotide microarrays was analyzed (Schwartz et al., 2002). In total, 73 genes, expressed 2- to 29-fold higher in clear cell ovarian carcinoma compared with each of the other ovarian carcinoma types, were identified.
Example 1 gene identifier list
Example 2. Comprehensive Gene Expression Analysis of Prostate Cancer Reveals Distinct Transcriptional Programs Associated with Metastatic Disease
This study (LaTulippe et al., 2002) performs a comprehensive gene expression analysis of prostate cancer using oligonucleotide arrays with 63,175 probe sets to identify genes with strong differential expression between non-recurrent primary prostate cancers and metastatic prostate cancers. Among highly ranked over-expressed genes (73 genes selected based on the t test statistic) by manual analyses the authors found genes that participate in cell cycle regulation, DNA replication, and DNA repair. Standard functional profiling of these genes reveals statistically significant enrichments related to several GO terms.
Example 2 gene identifier list
Example 3. Patterns of Gene Expression in Different Histotypes of Epithelial Ovarian Cancer Correlate with Those in Normal Fallopian Tube, Endometrium, and Colon
Microarray analysis was done to compare gene expression in 50 ovarian cancer specimens, including all four histotypes to gene expression in 5 pools of normal ovarian surface epithelial cells (Marquez et al., 2005). Data were analyzed to determine whether changes in gene expression correlated with different histotypes, grade, or stage.
Several set of genes that show the greatest ability to differentiate between considered cancer subtypes were originally identified. For example, 47 selected genes were 2-fold differentially expressed in mucinous ovarian cancers compared to other histotypes and with normal ovarian surface epithelial cells.
Example 3 gene identifier list
Example 4. Exploration of Global Gene Expression Patterns in Pancreatic Adenocarcinoma Using cDNA Microarrays
This study (Iacobuzio-Donahue et al., 2003) used cDNA microarrays to analyze global gene expression patterns in 14 pancreatic cancer cell lines, 17 resected infiltrating pancreatic cancer tissues, and 5 samples of normal pancreas to identify genes (125 genes) that are differentially expressed. Standard functional profiling of these genes reveals statistically significant enrichments of several GO terms.
Example 4 gene identifier list
Other Profiling tools
- Iacobuzio-Donahue,C.A., Maitra,A., Olsen,M., Lowe,A.W., van Heek,N.T., Rosty,C., Walter,K., Sato,N., Parker,A., Ashfaq,R., Jaffee,E., Ryu,B., Jones,J., Eshleman,J.R., Yeo,C.J., Cameron,J.L., Kern,S.E., Hruban,R.H., Brown,P.O., and Goggins,M. (2003). Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. Am. J. Pathol. 162, 1151-1162.
- LaTulippe,E., Satagopan,J., Smith,A., Scher,H., Scardino,P., Reuter,V., and Gerald,W.L. (2002). Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease. Cancer Res. 62, 4499-4506.
- Marquez,R.T., Baggerly,K.A., Patterson,A.P., Liu,J., Broaddus,R., Frumovitz,M., Atkinson,E.N., Smith,D.I., Hartmann,L., Fishman,D., Berchuck,A., Whitaker,R., Gershenson,D.M., Mills,G.B., Bast,R.C., Jr., and Lu,K.H. (2005). Patterns of gene expression in different histotypes of epithelial ovarian cancer correlate with those in normal fallopian tube, endometrium, and colon. Clin. Cancer Res. 11, 6116-6126.
- Schwartz,D.R., Kardia,S.L., Shedden,K.A., Kuick,R., Michailidis,G., Taylor,J.M., Misek,D.E., Wu,R., Zhai,Y., Darrah,D.M., Reed,H., Ellenson,L.H., Giordano,T.J., Fearon,E.R., Hanash,S.M., and Cho,K.R. (2002). Gene expression in ovarian cancer reflects both morphology and biological behavior, distinguishing clear cell from other poor-prognosis ovarian carcinomas. Cancer Res. 62, 4722-4729.