- R - statistical programming language
- most common statistical functions (t-test, ANNOVA, etc.) are built in
- Bioconductor - suite of R packages used for bioinformatic 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
- 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
Microarray Annotation Resources:
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