Function Reference

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Gene
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Description
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Anchored Bicliques of Biomolecular Associates
X
X
X
Genes
Highly similar genes, highly connected gene sets. Find genes that are connected to similar genes sets as your input genes. Degree threshold
Similar Gene Sets
X
1 Gene Set
Ranked list of similar gene sets (top 500) Rank all gene sets by similarity to a given gene set.
HiSim Graph
X
X
X
Gene Sets
Graph of hierarchical intersections of gene sets Generate directed acyclic graph of intersecting gene sets. Bootstraps

Permutations

Stopping rules

Gene Set Graph
X
X
X
Gene Sets
High degree connectivity of genes to your gene sets Plot the bipartite graph of gene sets. Degree threshold
Jaccard Similarity
X
X
Gene Sets
Matrix of pair-wise Venn diagrams and Jaccard similarity scores Pair-wise similarity of gene sets.
Hypergeometric Tests
X
X
Gene Sets
Matrix of pair-wise Venn diagrams and Jaccard similarity scores Pair-wise similarity of gene sets.
Jaccard Clustering
X
Gene Sets
Dendogram and cluster heat map revealing gene set similarity. Similarity clustering of gene sets. Clustering method.
Combine X
Gene Sets
Adjaceny matrix Create a matrix of genes and gene lists
Emphasis Genes
X
Genes
Highlight genes of interest on GeneSet Graph and HiSim Graph output
Boolean Gene Set Logic X
Gene Sets
Gene set consisting of union, intersection or highly connected genes from a group of gene sets. Condense a large number of gene sets into a single gene set based on connectivity, e.g. to find the intersection of multiple QTL positional candidates, or the union of all genes annotated to a set of related biological functions. Connectivity threshold

All functions are available from the “Analyze GeneSets” page, except for ABBA and Similar Gene Sets, which are accessed from the “Search for Genes” menu and “GeneSet Pages”, respectively. Emphasis Genes may be accessed from either “Analyze GeneSets” or any “Gene Set Page”

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