Massive Data Sources Mehmet Tevfik DORAK MD Ph

Massive Data Sources - Bio. Marts and FTP Sites UCSC, Ensembl, NCBI - Web

Massive Data UCSC Table Browser: http: //genome. ucsc. edu/cgi-bin/hg. Tables ENCODE Annotated Genomic regions:

Massive Data Enhancers list as BED file by cell type and location: http: //slidebase.

Bio. Marts: Ensembl ? http: //www. ensembl. org/biomart

Bio. Marts: UCSC http: //genome. ucsc. edu/cgi-bin/hg. Tables

Bio. Marts: GWAS Central http: //mart. gwascentral. org/biomart/martview

Databases Almost everybody database allows you to download their datasets.

Existing Collections of Data Even more datasets from mice!

Galaxy: Shared Data Library https: //usegalaxy. org/library

… Looking forward …. . YOUR FUTURE STARTS WITH HOPE

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Massive Data Sources Mehmet Tevfik DORAK, MD Ph. D 2 nd Practical Bioinformatics Course Istanbul, 17/18 April 2017 YOUR FUTURE STARTS WITH HOPE

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Massive Data Sources - Bio. Marts and FTP Sites UCSC, Ensembl, NCBI - Web Portals of Major Projects ENCODE, Road. Map Epigenomics Project, IHEC - Online Databases - Existing Collections in Databases Gene. Network-UTHSC, Imm. Port - Supplementary Data Files of Published Papers - Galaxy Shared Data

Massive Data UCSC Table Browser: http: //genome. ucsc. edu/cgi-bin/hg. Tables ENCODE Annotated Genomic regions: https: //www. encodeproject. org/data/annotations db. SNP list by chromosome: See GMail: db. SNP Data Download HGDP SNP data: http: //www. hagsc. org/hgdp/files. html NIEHS SNP Data Download: http: //egp. gs. washington. edu/data_download. html GRASP (QTL) results: http: //apps. nhlbi. nih. gov/Grasp/Updates. aspx GRASP (Full GWAS Results): https: //grasp. nhlbi. nih. gov/Full. Results. aspx FANTOM 5: http: //fantom. gsc. riken. jp/5/data db. SUPER Super Enhancers mi. RNA targets: mi. RTar. Base: http: //mirtarbase. mbc. nctu. edu. tw/php/download. php CAGE e. QTL SQLite database (and R query template): http: //cnsgenomics. com/shiny/CAGE Cell. Miner: https: //discover. nci. nih. gov/cellminer/load. Download. do d. Sys. Map: http: //dsysmap. irbbarcelona. org/download. php CADD scores: http: //cadd. gs. washington. edu/download DANN scores: https: //cbcl. ics. uci. edu/public_data/DANN/data EIGEN scores: http: //www. columbia. edu/~ii 2135/download. html Regulome. DB scores: http: //regulomedb. org/downloads db. WGFP Scores: http: //bioinfo. au. tsinghua. edu. cn/dbwgfp/downloads. php? page=downlite Geno. Canyon Predictive Scores: http: //genocanyon. med. yale. edu/Geno. Canyon_Downloads. html GERP scores: http: //mendel. stanford. edu/Sidow. Lab/downloads/gerp Fun. Seq 2 scores: http: //funseq 2. gersteinlab. org/downloads

Massive Data Enhancers list as BED file by cell type and location: http: //slidebase. binf. ku. dk PAZAR Transcription Factor Targets etc: http: //www. pazar. info/cgi-bin/downloads. pl TRRUST TFBSs database: http: //www. grnpedia. org/trrust/downloadnetwork. php Swiss Regulon Data: http: //swissregulon. unibas. ch/fcgi/sr/downloads (incl TFBSs) Broad Institute: https: //www. broadinstitute. org/scientific-community/data/H GTEx datasets: http: //www. gtexportal. org/home/datasets 2 Chicago e. QTL datasets (RNA-seq included): http: //eqtl. uchicago. edu/Home. html Hap. Map: http: //hapmap. ncbi. nlm. nih. gov/downloads/index. html. en (ftp: //ftp. ncbi. nlm. nih. gov/hapmap) LS-SNP Large Scale Human SNP Annotation: http: //modbase. compbio. ucsf. edu/LS-SNP/Downloads. html SNPs 3 D: http: //www. snps 3 d. org/download (incl. gene x gene inrerations) KD 4 v: http: //decrypthon. igbmc. fr/kd 4 v/cgi-bin/download (May be a dead link) Scientific data sources: https: //mran. revolutionanalytics. com/documents/data/#science Gencode data: http: //www. gencodegenes. org/releases/current. html Immune Cell Science Bio. Data Repository [Roederer, 2015 #5325]: ftp: //twinr-ftp. kcl. ac. uk/Immune. Cell. Science Cancer Genomics Hub (CGHub): https: //cghub. ucsc. edu/summary_stats. html (https: //cghub. ucsc. edu) Various genomics datasets from Fun. Seq website (see README file for descriptions): http: //funseq. gersteinlab. org/data Pre-computed Structure-PPi scores for COSMIC and 1 KG mutations: http: //structureppi. bioinfo. cnio. es/Structure Broad Institute Catalogs (TUCP, linc. RNA etc): http: //www. broadinstitute. org/genome_bio/human_lincrnas/? q=TUCP_transcripts_catalog Broad Institute Transcriptome Assemblies Download: http: //www. broadinstitute. org/genome_bio/human_lincrnas/? q=Transcriptome_Assemblies Broad Institute RNA-seq Read Alignments (Illumina Body Map): http: //www. broadinstitute. org/genome_bio/human_lincrnas/? q=Alignments SEER: http: //seer. cancer. gov/resources Large health-related data sets: http: //www. ehdp. com Personal Genome Project / Harvard: http: //www. personalgenomes. org/harvard/data Open SNP: Download the annotation dump: Includes annotation for all SNPs from all sources: https: //opensnp. org/data/annotation. zip (via https: //opensnp. org/snps) Phe. WAS dataset download: https: //phewas. mc. vanderbilt. edu/datatable HGNC download (http: //www. genenames. org): Download our ready-made data files from our Statistics and Downloads page, create your own datasets using either our Custom Downloads tool or Bio. Mart service, or write a script/program utilising our REST service.

Bio. Marts: Ensembl ? http: //www. ensembl. org/biomart

Bio. Marts: Ensembl http: //www. ensembl. org/biomart

Bio. Marts: UCSC http: //genome. ucsc. edu/cgi-bin/hg. Tables

Bio. Marts: GWAS Central http: //mart. gwascentral. org/biomart/martview

Web Portals of Major Projects