ARACNE

ベイジアンネットワークを改良したネットワーク解析アルゴリズム。遺伝子間の相互作用の強さを評価して、間接的な相互作用とみなせる関係を排除し、直接的な相互作用を高い精度で推定することを目指した。

ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

On synthetic datasets ARACNE achieves extremely low error rates and significantly outperforms established methods, such as Relevance Networks and Bayesian Networks. Application to the deconvolution of genetic networks in human B cells demonstrates ARACNE’s ability to infer validated transcriptional targets of the c-MYC proto-oncogene.

Ex）ヒトB細胞の遺伝子間相互作用推定

Reverse engineering of regulatory networks in human B cells. Nature Genetics. 2005 Apr;37(4):382-90. (Download PDF)

PANTHER Classification system

遺伝子、タンパク、パスウェイ等の公開データベース。

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological processontology terms. For an increasing number of proteins, detailed biochemical interactions in canonical pathways are captured and can be viewed interactively.To get started, try either a text search, browsing by function, or take a look at interactive pie charts that summarize the functions of whole genomes for Human, Mouse, Rat and Drosophila melanogaster.
PANTHER is supported by a research grant from the National Institute of General Medical Sciences [grant GM081084] and maintained by theEvolutionary Systems Biology Group at SRI.

Our database of genes, transcripts and proteins in the following species: Human, Mouse, Rat, and Drosophila melanogaster. Search by keyword Search by location Browse by function More...

A library (PANTHER/LIB) of protein families and subfamilies and associated data such as phylogenetic trees, multiple sequence alignments and HMMs. Search PANTHER Families Score a sequence against PANTHER HMMs More...

A database of 165 expert-curated signaling and metabolic pathways mapped to protein sequences in PANTHER Library, viewable in standard CellDesigner notation, a simplified activity flow notation, and Systems Biology Graphical Notation (SBGN) using our interactive pathway applet. Browse Pathways Search Pathways More...

A collection of terms (PANTHER/X) describing protein molecular functions and biological processes. Browse ontologies PANTHER to Gene Ontology™ mapping Gene Ontology™ to PANTHER mapping

マイクロアレイのパスウェイ解析も可能。