Avi Ma’ayan

Gene Set Knowledge Discovery with Enrichr

Abstract Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of genes and pro...

Lists2Networks: Integrated analysis of gene/protein lists

Lists2Networks is a user friendly web-based software system expected to significantly ease the computational analysis process for experimental systems biologists employing high-...

Genes2FANs: connecting genes through functional association networks

Abstract Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally i...

Sets2Networks: network inference from repeated observations of sets

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

Abstract Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks. ChIP-X E...

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

Abstract Motivation: Experiments such as ChIP-chip, ChIP-seq, ChIP-PET and DamID (the four methods referred herein as ChIP-X) are used to profile the binding of transcription fa...

KEA: kinase enrichment analysis

Abstract Motivation: Multivariate experiments applied to mammalian cells often produce lists of proteins/genes altered under treatment versus control conditions. Such lists can ...

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

Abstract Motivation: Genome-wide mRNA profiling provides a snapshot of the global state of cells under different conditions. However, mRNA levels do not provide direct understan...