Difference between revisions of "FlyBase:Drosophila Network Resources"

From FlyBase Wiki
Jump to: navigation, search
(Miscellaneous)
(Transcription Regulation Databases and Tools)
 
(28 intermediate revisions by 2 users not shown)
Line 19: Line 19:
 
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
 
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
 
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[http://chopchop.cbu.uib.no// Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
 
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[http://chopchop.cbu.uib.no// Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
* <b>CRISPOR</b> Model organism gRNA design tool:<br />[http://tefor.net/crispor/crispor.cgi/ TEFOR, Gif-sur-Yvette, France]
 
 
* <b>CRISPR/Cas Web Resources</b> Web Resources for design and planning of CRISPR/Cas9 studies:<br />[http://igtrcn.org/knowledgebase/crisprcas-web-resources// IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA]
 
* <b>CRISPR/Cas Web Resources</b> Web Resources for design and planning of CRISPR/Cas9 studies:<br />[http://igtrcn.org/knowledgebase/crisprcas-web-resources// IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA]
 
* <b>CRISPR-ERA</b> A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:<br />[http://crispr-era.stanford.edu// Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA]
 
* <b>CRISPR-ERA</b> A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:<br />[http://crispr-era.stanford.edu// Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA]
Line 34: Line 33:
 
* <b>Mojo Hand</b>, A TALEN Design Tool:<br />[http://www.talendesign.org/ Ekker lab, Mayo Clinic, Rochester, MN, USA]
 
* <b>Mojo Hand</b>, A TALEN Design Tool:<br />[http://www.talendesign.org/ Ekker lab, Mayo Clinic, Rochester, MN, USA]
 
* <b>OXfCRISPR</b>, Oxford Fly CRISPR Resources:<br />[https://www.dpag.ox.ac.uk/research/liu-group/liu-group-news/oxfcrispr Liu lab, University of Oxford, Oxford, UK]
 
* <b>OXfCRISPR</b>, Oxford Fly CRISPR Resources:<br />[https://www.dpag.ox.ac.uk/research/liu-group/liu-group-news/oxfcrispr Liu lab, University of Oxford, Oxford, UK]
* <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[http://ec2-54-88-183-115.compute-1.amazonaws.com/ Bulyk Lab, Harvard Medical School, Boston, MA, USA]
+
* <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[https://galaxyproject.org/use/sifted/ Bulyk Lab, Harvard Medical School, Boston, MA, USA]
 
* <b>TALengineering.org</b>, A Comprehensive Resource for Engineered TAL Effector Technology:<br />[http://talengineering.org/ Ekker lab, Joung Lab, MGH, Boston, USA]
 
* <b>TALengineering.org</b>, A Comprehensive Resource for Engineered TAL Effector Technology:<br />[http://talengineering.org/ Ekker lab, Joung Lab, MGH, Boston, USA]
 
* <b>ZiFiT Targeter</b>, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:<br />[http://zifit.partners.org/ZiFiT/ MGH and Harvard Medical School, Boston, MA]
 
* <b>ZiFiT Targeter</b>, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:<br />[http://zifit.partners.org/ZiFiT/ MGH and Harvard Medical School, Boston, MA]
Line 51: Line 50:
 
* <b>modERN</b>, model organism Encyclopedia of Regulatory Networks:<br />[http://epic.gs.washington.edu/modERN/ modERN, University of Washington, Seattle, USA]
 
* <b>modERN</b>, model organism Encyclopedia of Regulatory Networks:<br />[http://epic.gs.washington.edu/modERN/ modERN, University of Washington, Seattle, USA]
 
* <b>NCBI</b>, National Center for Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA]
 
* <b>NCBI</b>, National Center for Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA]
* <b>NCBI Map Viewer</b>, A genome view of Drosophila melanogaster:<br />[http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7227 NCBI, Bethesda, USA]
+
* <b>NCBI Genome Data Viewer</b>, A genome view of Drosophila melanogaster:<br />[https://www.ncbi.nlm.nih.gov/genome/gdv/?org=drosophila-melanogaster NCBI, Bethesda, USA]
 
* <b>PubMed</b>, Biomedical literature full-text archive:<br />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, USA]
 
* <b>PubMed</b>, Biomedical literature full-text archive:<br />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, USA]
 
* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
 
* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
Line 92: Line 91:
 
* <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 
* <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[http://bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
 
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[http://bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
* <b>Flannotator</b>, Annotation of Gene Expression:<br />[http://www.flyprot.org/index.php FlyAnnotator, University of Cambridge, UK]
 
 
* <b>FlyAtlas2</b>, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[http://flyatlas.gla.ac.uk/flyatlas/index.html FlyAtlas2, University of Glasgow, Glasgow, UK]
 
* <b>FlyAtlas2</b>, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[http://flyatlas.gla.ac.uk/flyatlas/index.html FlyAtlas2, University of Glasgow, Glasgow, UK]
* <b>FlyEx</b>, a Database of Segmentation Gene Expression in Drosophila:<br />[http://urchin.spbcas.ru/flyex/ FlyEx, St. Petersburg State Polytechnical University, Russia]
 
 
* <b>FlyExpress</b>, an Expression Pattern Search Engine:<br />[http://www.flyexpress.net/ FlyExpress, Arizona State University, USA]
 
* <b>FlyExpress</b>, an Expression Pattern Search Engine:<br />[http://www.flyexpress.net/ FlyExpress, Arizona State University, USA]
 
* <b>Fly-FISH</b>, A Database of Drosophila Embryo mRNA Localizaton Patterns:<br />[http://fly-fish.ccbr.utoronto.ca/ Fly-FISH, University of Toronto, Toronto, Canada]
 
* <b>Fly-FISH</b>, A Database of Drosophila Embryo mRNA Localizaton Patterns:<br />[http://fly-fish.ccbr.utoronto.ca/ Fly-FISH, University of Toronto, Toronto, Canada]
Line 103: Line 100:
 
* <b>Gene Expression Levels by Cell Line</b> (based on modENCODE data):<br />[http://www.flyrnai.org/cgi-bin/RNAi_expression_levels.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>Gene Expression Levels by Cell Line</b> (based on modENCODE data):<br />[http://www.flyrnai.org/cgi-bin/RNAi_expression_levels.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
 
* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
+
* <b>MidExDB</b>, Drosophila CNS Midline Gene Expression Database:<br />[http://midline.bio.unc.edu/MDB_Home.aspx Crews laboratory, University of North Carolina, Chapel Hill, USA]
 
* <b>MidgutAtlas</b>, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:<br />[http://flyatlas.gla.ac.uk/MidgutAtlas/index.html Dow laboratory, University of Glascow, Scotland, UK]
 
* <b>MidgutAtlas</b>, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:<br />[http://flyatlas.gla.ac.uk/MidgutAtlas/index.html Dow laboratory, University of Glascow, Scotland, UK]
 
* <b>RNAMiner</b>, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:<br />[http://calla.rnet.missouri.edu/rnaminer/ Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA]
 
* <b>RNAMiner</b>, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:<br />[http://calla.rnet.missouri.edu/rnaminer/ Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA]
  
 
=Gene Groups=
 
=Gene Groups=
* <b>FlyBase Gene Groups</b>, Manually curated reports on functionally related genes, based on the literature:<br /> [http://flybase.org/static_pages/FBgg/browse.html Gene group list, FlyBase]
+
* <b>FlyBase Gene Groups</b>, Manually curated reports on functionally related genes, based on the literature:<br /> [http://flybase.org/lists/FBgg/ Gene group list, FlyBase]
 +
* <b>FlyBase Signaling Pathways</b>, Manually curated reports on Signaling Pathways, based on the literature:<br /> [http://flybase.org/lists/FBgg/pathways Pathways list, FlyBase]
 
* <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [http://www.flyrnai.org/tools/glad/web/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [http://www.flyrnai.org/tools/glad/web/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [http://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 
* <b>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [http://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
Line 129: Line 127:
 
=Genome Sequencing Projects=
 
=Genome Sequencing Projects=
 
* <b>''D. pseudoobscura'' genome project</b>:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA]
 
* <b>''D. pseudoobscura'' genome project</b>:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA]
* <b>''D. simulans'' genome project</b>:<br />[http://genome.wustl.edu/genomes/detail/drosophila-simulans-white-501/ D. simulans White 501 Genome Sequencing Center, Washington University, USA]
 
* <b>''D. yakuba'' genome project</b>:<br />[http://genome.wustl.edu/genomes/detail/drosophila-yakuba/ D. yakuba Genome Sequencing Center, Washington University, USA]
 
 
* <b>D. simulans and yakuba sequencing projects</b>:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA]
 
* <b>D. simulans and yakuba sequencing projects</b>:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA]
  
 
=Human Disease: Drosophila Models and Orthologous Genes=
 
=Human Disease: Drosophila Models and Orthologous Genes=
* <b>Bloomington Stock Center</b>, Drosophila and Human Disease page:<br />[http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm Bloomington Stock Center, Bloomington, IN, USA]
+
* <b>Bloomington Stock Center</b>, Drosophila and Human Disease page:<br />[https://bdsc.indiana.edu/stocks/hd/index.html Bloomington Stock Center, Bloomington, IN, USA]
 
* <b>DIOPT-DIST</b>, Disease-related Ortholog Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>DIOPT-DIST</b>, Disease-related Ortholog Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>Drosophila as a Model for Human Diseases</b>:<br />[http://www.sdbonline.org/sites/fly/modelsystem/aamodelsystem.htm Interactive Fly, Bethesda, MD, USA]
 
* <b>Drosophila as a Model for Human Diseases</b>:<br />[http://www.sdbonline.org/sites/fly/modelsystem/aamodelsystem.htm Interactive Fly, Bethesda, MD, USA]
Line 147: Line 143:
 
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>DAPPER</b>, database for protein-protein interactions:<br/>[http://dapper.gen.cam.ac.uk/ DAPPER, University of Cambridge, Cambridge, UK]
 
* <b>DAPPER</b>, database for protein-protein interactions:<br/>[http://dapper.gen.cam.ac.uk/ DAPPER, University of Cambridge, Cambridge, UK]
* <b>DPiM</b>, Drosophila Protein interaction Map:<br />Harvard University Medical School, Boston, MA, USA
+
* <b>DPiM</b>, Drosophila Protein interaction Map:<br/>[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
 
* <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 
* <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 
* <b>Drosophila PIMRider</b>, Drosophila Protein Interaction Map:<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
 
* <b>Drosophila PIMRider</b>, Drosophila Protein Interaction Map:<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
 +
* <b>FlyBase Signaling Pathways</b>, Manually curated reports on Signaling Pathways, based on the literature:<br /> [http://flybase.org/lists/FBgg/pathways Pathways list, FlyBase]
 
* <b>FlyCyc</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 
* <b>FlyCyc</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 
* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
* <b>FlyReactome</b> -- a Curated Knowledgebase of Drosophila melanogaster Pathways:<br />[http://fly.reactome.org FlyReactome, University of Cambridge, Cambridge, UK]
 
 
* <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
 
* <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
 
* <b>IntAct</b>, Molecular Interaction Database:<br />[http://www.ebi.ac.uk/intact/ IntAct, EMBL-EBI, Hinxton, UK]
 
* <b>IntAct</b>, Molecular Interaction Database:<br />[http://www.ebi.ac.uk/intact/ IntAct, EMBL-EBI, Hinxton, UK]
Line 207: Line 203:
 
===miRNA Target Prediction===
 
===miRNA Target Prediction===
 
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction (last updated 2014):<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
 
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction (last updated 2014):<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
* <b>MicroCosm Targets</b>, Computationally predicted targets for microRNAs across many species based on MiRanda algorithm (last updated 2007):<br />[http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ MicroCosm Targets, EMBL-EBI, Hinxton, UK]
+
* <b>MicroCosm Targets</b>, Computationally predicted targets for microRNAs across many species based on MiRanda algorithm (last updated 2007):<br />[http://didattica.cribi.unipd.it/genomica/Genomics_2013/9-mirna/Microcosm%20Targets.html MicroCosm Targets, EMBL-EBI, Hinxton, UK]
* <b>microRNA.org</b>, Predicted microRNA targets & target downregulation scores based on miRanda and mirSVR algorithms (last updated 2007):<br />[http://www.microrna.org/microrna/home.do microRNA.org, Memorial Sloan-Kettering Cancer Center, New York, NY, USA]
 
 
* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence (last updated 2010):<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence (last updated 2010):<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
* <b>miRNA - Target Gene Prediction</b> (last updated 2005):<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
 
 
* <b>miRNA_Targets</b> (last updated 2011):<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
 
* <b>miRNA_Targets</b> (last updated 2011):<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
 +
* <b>miRWalk - The Database on Predicted and Validated microRNA Targets</b> :<br />[http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk/micrornapredictedtarget.html miRNA - Target Prediction, Ruprecht-Karls-Universität Heidelberg, Medizinische Fakultät Mannheim, Germany]
 
* <b>TargetScanFly</b>, Prediction of microRNA targets based on miRNA seed region and target conservation (last updated 2012):<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, Cambridge, MA, USA]
 
* <b>TargetScanFly</b>, Prediction of microRNA targets based on miRNA seed region and target conservation (last updated 2012):<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, Cambridge, MA, USA]
  
 
===Validated miRNA Targets===
 
===Validated miRNA Targets===
* <b>DIANA TarBase</b>, MicroRNA Target Database (last updated 2014):<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index DIANA TarBase, DIANA LAB, Athens, Greece]
+
* <b>DIANA TarBase</b>, MicroRNA Target Database (last updated 2017):<br />[http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex DIANA TarBase, DIANA LAB, Athens, Greece]
 
* <b>miRecords</b>, A database of experimentally validated miRNA targets curated from literature (last updated 2009):<br />[http://c1.accurascience.com/miRecords/ miRecords, University of Minnesota, Minneapolis, MN, USA]
 
* <b>miRecords</b>, A database of experimentally validated miRNA targets curated from literature (last updated 2009):<br />[http://c1.accurascience.com/miRecords/ miRecords, University of Minnesota, Minneapolis, MN, USA]
* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database (last updated 2015):<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
 
 
* <b>miRTex</b>, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):<br />[http://research.bioinformatics.udel.edu/miRTex/ miRTex, University of Delaware, Newark, DE, USA]
 
* <b>miRTex</b>, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):<br />[http://research.bioinformatics.udel.edu/miRTex/ miRTex, University of Delaware, Newark, DE, USA]
  
Line 283: Line 277:
 
* <b>Drosophila Polymorphism Database</b>:<br />[http://dpdb.uab.es/dpdb/dpdb.asp DPDB, Universitat Autonoma de Barcelona, Barcelona, Spain]
 
* <b>Drosophila Polymorphism Database</b>:<br />[http://dpdb.uab.es/dpdb/dpdb.asp DPDB, Universitat Autonoma de Barcelona, Barcelona, Spain]
 
* <b>DPGP</b>, Drosophila Population Genomics Project:<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA]
 
* <b>DPGP</b>, Drosophila Population Genomics Project:<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA]
* <b>DSPR</b>, Drosophila Synthetic Population Resource:<br />[http://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA]
+
* <b>DSPR</b>, Drosophila Synthetic Population Resource:<br />[http://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA]* <b>FlyVar Project</b>: A Database of Drosophila Genetics Variations <br />[http://www.iipl.fudan.edu.cn/FlyVar/ FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA]
* <b>FlySNP Project</b>:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria]
 
* <b>FlyVar Project</b>: A Database of Drosophila Genetics Variations <br />[http://www.iipl.fudan.edu.cn/FlyVar/ FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA]
 
 
* <b>Global Diversity Lines</b>: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains<br />[http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP050151 Global Diversity Lines, Cornell University, Ithaca, NY, USA]
 
* <b>Global Diversity Lines</b>: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains<br />[http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP050151 Global Diversity Lines, Cornell University, Ithaca, NY, USA]
  
Line 300: Line 292:
 
* <b>RBPDB</b>, the database of RNA-binding protein specificities:<br />[http://rbpdb.ccbr.utoronto.ca/ RBPDB]  
 
* <b>RBPDB</b>, the database of RNA-binding protein specificities:<br />[http://rbpdb.ccbr.utoronto.ca/ RBPDB]  
 
* <b>SMART</b>, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, Protein Domain Analysis, EMBL, Heidleberg]
 
* <b>SMART</b>, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, Protein Domain Analysis, EMBL, Heidleberg]
* <b>UniProtKB</b>, a comprehensive catalog of information on proteins:<br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium]
+
* <b>UniProtKB</b>, a comprehensive catalog of information on proteins:<br />[https://www.uniprot.org/uniprot/ UniProtKB, The UniProt Consortium]
  
 
=Public Education=
 
=Public Education=
Line 347: Line 339:
  
 
=Transcription Regulation Databases and Tools=
 
=Transcription Regulation Databases and Tools=
* <b>BDTNP</b>, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
+
* <b>BDTNP</b>, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov:8080/Fly-Net/ Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 
* <b>CORE</b>, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/core-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
 
* <b>CORE</b>, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/core-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
 
* <b>DBD</b>, Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK]
 
* <b>DBD</b>, Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK]
Line 359: Line 351:
 
* <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, USA]
 
* <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, USA]
 
* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 
* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
* <b>The Drosophila Transcription Factor Database</b>:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK]
+
* <b>The Drosophila Transcription Factor Database</b>:<br />[https://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html FlyTF.org, MRC Cambridge, UK]
 
* <b>TRANSFAC</b>, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
 
* <b>TRANSFAC</b>, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
  
 
=Suggest a tool or resource=
 
=Suggest a tool or resource=
*Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact Flybase] to suggest a tool or resource for the list.
+
*Please [http://flybase.org/contact/email contact Flybase] to suggest a tool or resource for the list.
  
 
[[Category:DONE]]
 
[[Category:DONE]]

Latest revision as of 03:59, 29 March 2019

Atlases, Images and Videos

CRISPRs and TALENs

Data Repositories

Drosophila Genomes Data and Metadata

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Laboratory Resources

Miscellaneous

Non-coding (ncRNA) Databases and Tools

General

lncRNA

miRNA

General

NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.

miRNA Target Prediction

Validated miRNA Targets

Comparative miRNA Analysis

rRNA

tRNA

snoRNA

SRP RNA

Ontology Resources

Orthology Predictions

Phylogenetic Comparison Tools

Population Biology and Polymorphism Resources

Protein Analysis

Public Education

RNAi

Sequence Analysis

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource