1. Mehmet Tevfik DORAK, MD PhD 2nd Practical Bioinformatics Course
Massive Data Sources
Mehmet Tevfik DORAK, MD PhD
2nd Practical Bioinformatics Course
Istanbul, 17/18 April 2017

2. Schedule

3. Massive Data Sources - Existing Collections in Databases
- BioMarts and FTP Sites
UCSC, Ensembl, NCBI
- Web Portals of Major Projects
ENCODE, RoadMap Epigenomics Project, IHEC
- Online Databases
- Existing Collections in Databases
GeneNetwork-UTHSC, ImmPort
- Supplementary Data Files of Published Papers
- Galaxy Shared Data

4. Massive Data
UCSC Table Browser:
ENCODE Annotated Genomic regions:
dbSNP SNP list by chromosome: See GMail: dbSNP Data Download
HGDP SNP data:
NIEHS SNP Data Download:
GRASP (QTL) results:
GRASP (Full GWAS Results):
FANTOM5:
dbSUPER Super Enhancers
miRNA targets: miRTarBase:
CAGE eQTL SQLite database (and R query template):
CellMiner:
dSysMap:
CADD scores:
DANN scores:
EIGEN scores:
RegulomeDB scores:
dbWGFP Scores:
GenoCanyon Predictive Scores:
GERP scores:
FunSeq2 scores:

5. Massive Data
Enhancers list as BED file by cell type and location:
PAZAR Transcription Factor Targets etc:
TRRUST TFBSs database:
Swiss Regulon Data: (incl TFBSs)
Broad Institute:
GTEx datasets:
Chicago eQTL datasets (RNA-seq included):
HapMap: (ftp://ftp.ncbi.nlm.nih.gov/hapmap)
LS-SNP Large Scale Human SNP Annotation:
SNPs3D: (incl. gene x gene inrerations)
KD4v: (May be a dead link)
Scientific data sources:
Gencode data:
Immune Cell Science BioData Repository [Roederer, 2015 #5325]: ftp://twinr-ftp.kcl.ac.uk/ImmuneCellScience
Cancer Genomics Hub (CGHub): (
Various genomics datasets from FunSeq website (see README file for descriptions):
Pre-computed Structure-PPi scores for COSMIC and 1KG mutations:
Broad Institute Catalogs (TUCP, lincRNA etc):
Broad Institute Transcriptome Assemblies Download:
Broad Institute RNA-seq Read Alignments (Illumina Body Map):
SEER:
Large health-related data sets:
Personal Genome Project / Harvard:
Open SNP: Download the annotation dump: Includes annotation for all SNPs from all sources:
(via
PheWAS dataset download:
HGNC download (
Download our ready-made data files from our Statistics and Downloads page, create your own datasets using either
our Custom Downloads tool or BioMart service, or write a script/program utilising our REST service.

6. ? BioMarts: Ensembl http://www.ensembl.org/biomart
Ensembl BioMart:

7. BioMarts: Ensembl http://www.ensembl.org/biomart
Ensembl BioMart:

8. BioMarts: UCSC http://genome.ucsc.edu/cgi-bin/hgTables
UCSC BioMart:

9. BioMarts: UCSC http://genome.ucsc.edu/cgi-bin/hgTables
UCSC BioMart:

10. BioMarts: GWAS Central
GWAS Central GWASMart:

11. Web Portals of Major Projects
ENCODE Portal:
Paper:

12. Web Portals of Major Projects
RoadMap Epigenomics Project data portal:
Paper: (PMC:

13. Web Portals of Major Projects
RoadMap Epigenomics Project web portal:

14. Web Portals of Major Projects
IHEC data portal:

15. Web Portals of Major Projects
IHEC data portal: >>> Download page:

16. Web Portals of Major Projects
IHEC web portal (CELL):
Paper (CELL):

17. Almost everybody database allows you to download their datasets.
Databases
Almost everybody database allows you to download their datasets.
Links:
>>>

18. FunSeq: Downloads
Link:

19. dbNSFP: Downloads Paper: https://www.ncbi.nlm.nih.gov/pubmed/26555599
dbNSFP: (see also:

20. Existing Collections of Data Even more datasets from mice!
GeneNetwork:
Even more datasets from mice!

21. Existing Collections of Data
Oprn ImmPort:

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

23. Supplementary Data Files
Link:

24. Supplementary Data Files
Paper:
Suppl Tables (PMC):

25. … Looking forward …..