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GeneNetworkBuilder (version 1.14.3)

Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data

Description

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

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Version

Version

1.14.3

License

GPL (>= 2)

Maintainer

Jianhong Ou

Last Published

February 15th, 2017

Functions in GeneNetworkBuilder (1.14.3)

hs.miRNA.map

micro RNA of Homo sapiens
hs.mapIDs

map file for converting from Entrez identifier to Homo sapiens gene name
ce.mapIDs

map file for converting from wormbase identifier to Caenorhabditis elegans gene name
ce.miRNA.map

micro RNA of Caenorhabditis elegans
example.data

example datasets for documentation
ce.interactionmap

transcript regulatory map of Caenorhabditis elegans
hs.interactionmap

transcript regulation map of Homo sapiens
uniqueExprsData

unique the microarray data
polishNetwork

generate an object of grahpNEL to represent the regulation network
convertID

convert gene IDs by id map
hs.IDsMap

map file for converting gene name or sequence name of Homo sapiens to Entrez identifier
filterNetwork

filter the regulatory network table by expression profile
buildNetwork

construct the regulatory network
ce.IDsMap

map file for converting gene name or sequence name of Caenorhabditis elegans to wormbase identifier