Bioinformatics 101: Gene Expression Analysis

Differential Expression Tools:

• R - statistical programming language
• most common statistical functions (t-test, ANNOVA, etc.) are built in
• Bioconductor - suite of R packages used for bioinformatic analysis
• limma - most commonly used differential expression tool for microarray analysis
• edgeR - R package for RNA-Seq differential expression analysis
• DEseq - R package for RNA-Seq differential expression analysis
• cuffdiff
• differential expression package within cufflinks
• cufflinks provides transcript abundance calculations
• strictly speaking, the developers recommend using cuffdiff for differential expression, although it is relatively common to use edgeR, DEseq, etc. for differential expression following mRNA quantification via cufflinks
• Java TreeView
• free tool for clustering microarray data
• OCplus - R package for statistical power calculations (and differential expression) for microarray studies
• Scotty - web-based tool for statistical power calculations for RNA-Seq data
• Partek Genomics Suite
• Commercial program that includes a number of workflows, such as microarray gene expression and RNA-Seq analysis
• Includes statistics for differential expression analysis as well as tools for downstream functional analysis and upstream quality control assessment

lncRNA Resources:

• MiTranscriptome - known and novel lncRNAs with cancer-associated profiles
• TANRIC - TCGA and CCLE expression analysis for lncRNAs (including correlations with protein-coding genes and miRNAs)
• Expression Atlas - gene expression profiles for known genes across various datasets
• lncrnadb - includes additional annotations for known lncRNAs
• lncATLAS - contains subcellular location information for ENSEMBL-format lncRNAs for some cancer cell lines

Transcription Factor Motif Analysis:

• IPA Upstream Regulator Analysis
• Commercial tool that searches for enrichment of known targets for regulatory genes and molecules (such as transcription factors)
• Can also detect if targets are consistent with activation or inhibition of the regulator
• SCOPE
• free tool that identifies upstream motifs enriched for gene lists
• works on a wide variety of species, so it is useful for motif finding in less commonly studies organisms
• Whole Genome rVISTA - calculate enrichment of transcription factor motifs predicted based upon evolutionary conservation
• TRED (Transcriptional Regulatory Element Database) - database from CSHL for transcription factors.  Includes target gene lists for transcription factors in human, mouse, and rat
• TRANSFAC - database of transcription factor motif sequences.  There are commercial and open-source versions of the database
• JASPAR - open-source database of transcription factor motif sequences

General RNA-Seq Information:

• Wikipedia list of RNA-Seq bioinformatics tools

Microarray Annotation Resources:

• NetAffx
• Affymetrix resource for probe design information
• registration is free but required
• GeneAnnot
• an alternative resource for Affymetrix probe annotations