Literature and Links to sites mentioned in Lecture 11 (and pathways, and expression)

Literature

• Review of GO
  Use and misuse of the gene ontology annotations
  Rhee SY, Wood V, Dolinski K, Draghici S.
  Nat Rev Genet. 2008 Jul;9(7):509-15.

• Consistency of GO analysis over time
  Monitoring changes in the Gene Ontology and their impact on genomic data analysis
  Jacobson M, Sedeno-Cortes AS, Pavlidis P.
  GigaScience. 2018 August;7(8)

• Review of 68 gene enrichment tools
  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
  Huang da W, Sherman BT, Lempicki RA.
  Nucleic Acids Res. 2009 Jan;37(1):1-13.

• The Topology-weighted and Topolgy-elim algorithms
  Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
  Alexa A, Rahnenfuhrer J, Lengauer T.
  Bioinformatics. 2006 Jul 1;22(13):1600-7.

• The Parent-Child algorithms
  Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
  Grossmann S, Bauer S, Robinson PN, Vingron M.
  Bioinformatics. 2007 Nov 15;23(22):3024-31.

• MGSA algorithm
  GOing Bayesian: model-based gene set analysis of genome-scale data
  Bauer S, Gagneur J, Robinson PN.
  Nucleic Acids Research. 2010 Feb 19; 38(11):3523-3532.

• Ontologizer paper
  Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration
  Bauer S, Grossmann S, Vingron M, Robinson PN.
  Bioinformatics. 2008 Jul 15;24(14):1650-1.

• DAVID paper (including step-by-step instructions)
  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
  Huang da W, Sherman BT, Lempicki RA.
  Nat Protoc. 2009;4(1):44-57.

Some pathway related papers:

• Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
  Khatri P, Sirota M, Butte AJ
  PLOS Computational Biology, 2012 8(2):e1002375.

• Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?
  Wood V, Lock A, Harris MA, Rutherford K, Bahler J, Oliver SG.
  Open Biology, 2019 9(2):180241.

• Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
  Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD.
  Nature Protocols, 2019 14:482-517

• WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs
  Liao Y, Wang J, Jaehnig EJ, Shi Z, Zhang B.
  Nucleic Acids Research, 2019 47(W1):W199-W205

• g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)
  Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, Vilo J.
  Nucleic Acids Research, 2019 47(W1):W191-W198

Links

Selected GO databases:

• Gene Ontology Consortium website: http://www.geneontology.org/
• Amigo: http://amigo.geneontology.org/
• GOA: http://www.ebi.ac.uk/GOA/
• QuickGo: https://www.ebi.ac.uk/QuickGO/

Selected Pathway databases:

• KEGG (Kyoto Encyclopedia of Genes and Genomes): https://www.genome.jp/kegg/
• BioCyc: https://biocyc.org
• Reactome: https://reactome.org
• Wikipathways: https://www.wikipathways.org/index.php/WikiPathways

GO and Pathway tools:

• Ontologizer 2.0: http://www.ontologizer.de
• DAVID: http://david.ncifcrf.gov/
• WebGestalt: http://www.webgestalt.org/
• g:Profiler: https://biit.cs.ut.ee/gprofiler/gost
• Metascape: https://metascape.org/
• GSEA: http://software.broadinstitute.org/gsea/index.jsp
• Cytoscape: https://cytoscape.org/

Various Expression Databases:

• https://www.ncbi.nlm.nih.gov/geo/ NCBI GEO a repository for microarray and sequencing data
• https://www.ebi.ac.uk/gxa/home EBI GXA: Gene Expression Atlas
• https://www.ebi.ac.uk/gxa/sc/home EBI GXA for single cell data
• http://www.informatics.jax.org/expression.shtml Mouse Genome Informatics Expression Data
• https://gtexportal.org/home/ GTEx portal
• https://www.proteinatlas.org/ Human Protein Atlas
• https://pax-db.org/ PaxDb: Protein Abundance Database
• https://netbio.bgu.ac.il/tissuenet3/ TissueNet V.3 - Human Tissue protein-protein interactions
• http://biogps.org/ BioGPS
• https://coxpresdb.jp/ COXPRESdb co-expression information for various species
• https://planex.plantbioinformatics.org/ Planex - plant co-expression database
• http://portal.brain-map.org/ Allen Brain Map
• https://research.cchmc.org/pbge/lunggens/mainportal.html LGEA Web Portal: Lung Gene Expression Analysis
• https://www.humancellatlas.org/ Human Cell Atlas
• http://jinglebells.bgu.ac.il/ RNA-Seq database (single cell)
• http://single-cell.clst.riken.jp/ SCPortalen: Single-cell centric database
• https://panglaodb.se/ PanglaoDB single cell database, including suggested marker genes
• https://www.proteomicsdb.org/ ProteomicsDB - human proteomics data
• http://www.peptideatlas.org/ Peptide Altas
• https://www.subcellbarcode.org/ SUBCELL Barcode - proteome subcellular localization
• https://alganaut.uts.edu.au/ Alganaut - transcriptomics for Algae
• http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi Arabidopsis eFP Browser

Others:

• Identifier Conversion Tools: http://bip.weizmann.ac.il/toolbox/seq_analysis/annotation.html