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
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.