Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion.
When the same set of genes appear in two top ranking gene lists in two different studies, it is often of interest to estimate the probability for this being a chance event. This overlapping probability is well known to follow the hypergeometric distribution. Usually, the lengths of top-ranking gene lists are assumed to be fixed, by using a pre-set criterion on, e.g., p-value for the t-test. We investigate how overlapping probability changes with the gene selection criterion, or simply, with the length of the top-ranking gene lists. It is concluded that overlapping probability is indeed a function of the gene list length, and its statistical significance should be quoted in the context of gene selection criterion.
Fury
Wen
W
Regeneron Pharmaceutical Inc., Tarrytown, NY 10591, USA. wen.fury@regeneron.com
Batliwalla
Franak
F
Gregersen
Peter K
PK
Li
Wentian
W
D000465:Algorithms; D016000:Cluster Analysis; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D010363:Pattern Recognition, Automated; D011336:Probability; D012984:Software