Bioinformatics Tutorial
Files Needed
  • Getting Started
    • Setup
    • Run jobs in a Docker
    • Run jobs in a cluster [Advanced]
  • Part I. Programming Skills
    • 1.Linux
      • 1.1.Basic Command
      • 1.2.Practice Guide
      • 1.3.Linux Bash
    • 2.R
      • 2.1.R Basics
      • 2.2.Plot with R
    • 3.Python
  • PART II. BASIC ANALYSES
    • 1.Blast
    • 2.Conservation Analysis
    • 3.Function Analysis
      • 3.1.GO
      • 3.2.KEGG
      • 3.3.GSEA
    • 4.Clinical Analyses
      • 4.1.Survival Analysis
  • Part III. NGS DATA ANALYSES
    • 1.Mapping
      • 1.1 Genome Browser
      • 1.2 bedtools and samtools
    • 2.RNA-seq
      • 2.1.Expression Matrix
      • 2.2.Differential Expression with Cufflinks
      • 2.3.Differential Expression with DEseq2 and edgeR
    • 3.ChIP-seq
    • 4.Motif
      • 4.1.Sequence Motif
      • 4.2.Structure Motif
    • 5.RNA Network
      • 5.1.Co-expression Network
      • 5.2.miRNA Targets
      • 5.3. CLIP-seq (RNA-Protein Interaction)
    • 6.RNA Regulation - I
      • 6.1.Alternative Splicing
      • 6.2.APA (Alternative Polyadenylation)
      • 6.3.Chimeric RNA
      • 6.4.RNA Editing
      • 6.5.SNV/INDEL
    • 7.RNA Regulation - II
      • 7.1.Translation: Ribo-seq
      • 7.2.RNA Structure
    • 8.cfDNA
      • 8.1.Basic cfDNA-seq Analyses
  • Part IV. MACHINE LEARNING
    • 1.Machine Learning Basics
      • 1.1 Data Pre-processing
      • 1.2 Data Visualization & Dimension Reduction
      • 1.3 Feature Extraction and Selection
      • 1.4 Machine Learning Classifiers/Models
      • 1.5 Performance Evaluation
    • 2.Machine Learning with R
    • 3.Machine Learning with Python
  • Part V. Assignments
    • 1.Precision Medicine - exSEEK
      • Help
      • Archive: Version 2018
        • 1.1.Data Introduction
        • 1.2.Requirement
        • 1.3.Helps
    • 2.RNA Regulation - RiboShape
      • 2.0.Programming Tools
      • 2.1.RNA-seq Analysis
      • 2.2.Ribo-seq Analysis
      • 2.3.SHAPE Data Analysis
      • 2.4.Integration
    • 3.RNA Regulation - dsRNA
    • 4.Single Cell Data Analysis
      • Help
  • 5.Model Programming
  • Appendix
    • Appendix I. Keep Learning
    • Appendix II. Databases & Servers
    • Appendix III. How to Backup
    • Appendix IV. Teaching Materials
    • Appendix V. Software and Tools
    • Appendix VI. Genome Annotations
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On this page
  • 1) Projects
  • 2) Databases
  • (1) General
  • (2) Expression Data
  • (3) Exosomal database
  • 3) Servers
  • (1) General
  • (2) Gene functional analysis
  • (3) RNA secondary structure
  • (4) miRNA targets prediction
  • (5) Sequence motif analysis

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  1. Appendix

Appendix II. Databases & Servers

PreviousAppendix I. Keep LearningNextAppendix III. How to Backup

Last updated 4 years ago

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1) Projects

  • ENCODE

    Encyclopedia of DNA Elements: a comprehensive parts list of functional elements in the human genome.

  • 1000 Genomes

    most genetic variants with frequencies of at least 1% in the populations studied.

  • TCGA

    The Cancer Genome Atlas: From the analysis of over 11,000 tumors from 33 of the most prevalent forms of cancer, the Pan-Cancer Atlas provides a uniquely comprehensive, in-depth, and interconnected understanding of how, where, and why tumors arise in humans. As a singular and unified point of reference, the Pan-Cancer Atlas is an essential resource for the development of new treatments in the pursuit of precision medicine.

  • CCLE (cancer cell lines)

    Cancer Cell Line Encyclopedia

    • CCLE RNA-seq BAM files:[[)

  • ICGC

  • Other Integrative Projects

2) Databases

(1) General

  1. NCBI

  2. UCSC

  3. Ensemble

(2) Expression Data

  1. GTEx

  2. Expression Atlas

  3. GEPIA

  4. cBioPortal

  5. TCGA ncRNA

(3) Exosomal database

1.ExoCarta

2.exoRBase

3.EVmiRNA

4.EV-TRACK

5.EVpedia

6.Vesiclepedia

7.EMBL-EBI

8.Urinary Exosome Protein Database

3) Servers

(1) General

  1. BLAST

(2) Gene functional analysis

  1. David

  2. KAAS

(3) RNA secondary structure

  1. RNAfold

  2. RNAstructure

(4) miRNA targets prediction

  1. TargetScan

  2. psRNATarget

(5) Sequence motif analysis

contribute to the NIH mission of ‘uncovering new knowledge’.

genome browser for vertebrate.

genome annotation.

gene expression in different tissues.

exploring gene expression results across species under different biological conditions.

gene expression in different TCGA tumor types.

visualization, analysis and download of large-scale cancer genomics data sets.

​

A web-based compendium of exosomal cargo.

A repository of circular RNA (circRNA), long non-coding RNA (lncRNA) and messenger RNA (mRNA) derived from RNA-seq data analyses of human blood exosomes. Experimental validations from published literature are also included.

A database of miRNA profiling in extracellular vesicles.

Transparent reporting and centralizing knowledge in extracellular vesicle research.

An integrated database of high-throughput data for systemic analyses of extracellular vesicles. A community web portal for extracellular vesicles research.

A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 12, e1001450.

The EMBL-EBI exosomes database is a comprehensive annotated database of GO function analysis of human exosomal proteins. The database works closely with laboratory researchers (Dr S Mathivanan - La Trobe Institute, Dr A Kalea - UCL) and the exosomal database Exocarta () and Vesiclepedia to identify annotations for focus Annotation of the target protein as well as the experimental methodology of the exosomes.

This database of urinary exosome proteins is based on published protein mass spectrometry data from the NHLBI Epithelial Systems Biology Laboratory (ESBL). All data are from urinary exosomes isolated from healthy human volunteers.

finds regions of similarity between biological sequences.

gene functional classification tool.

KEGG Automatic Annotation Server.

predict secondary structures of single stranded RNA or DNA sequences.

RNA secondary structure prediction and analysis.

search for predicted microRNA targets in mammals

plant small RNA target analysis

MEME motif based sequence analysis tools

https://www.encodeproject.org/
http://www.internationalgenome.org/
portal
Cell papers
TCGA Research Network
TCGA data portal
Pan-TCGA
Broad GDAC Firehose
Broad GDAC FireBrowse
TCGA/GTEx: Schultz Lab
Normalized data
TCGA/GTEx: GEPIA 2
CCLE
https://portal.gdc.cancer.gov/legacy-archive/search/f?filters={"op":"and","content":[{"op":"in","content":{"field":"cases.project.program.name","value":["CCLE"]}}]}](https://portal.gdc.cancer.gov/legacy-archive/search/f?filters={"op":"and","content":[{"op":"in","content":{"field":"cases.project.program.name","value":["CCLE"]}}]}](https://portal.gdc.cancer.gov/legacy-archive/search/f?filters={"op":"and","content":[{"op":"in","content":{"field":"cases.project.program.name","value":["CCLE"]}}]}]%28https://portal.gdc.cancer.gov/legacy-archive/search/f?filters={"op":"and","content":[{"op":"in","content":{"field":"cases.project.program.name","value":["CCLE"]}}]})\
CCLE Raw data
CCLE Seven Bridges
ICGC
PCAWG
COSMIC
UCSC Xena
cBioPortal
MSK-IMPACT
OncoKB
https://www.ncbi.nlm.nih.gov/
https://genome.ucsc.edu/
http://www.ensembl.org/index.html
https://www.gtexportal.org/home/
https://www.ebi.ac.uk/gxa/home
http://gepia.cancer-pku.cn/index.html
http://www.cbioportal.org/index.do
http://ibl.mdanderson.org/tanric/_design/basic/index.html
http://www.exocarta.org/
http://www.exorbase.org/
http://bioinfo.life.hust.edu.cn/EVmiRNA
http://www.evtrack.org/
http://evpedia.info
http://www.microvesicles.org/
http://www.exocarta.org/
https://hpcwebapps.cit.nih.gov/ESBL/Database/Exosome/
https://blast.ncbi.nlm.nih.gov/Blast.cgi
https://david.ncifcrf.gov/
https://www.genome.jp/kegg/kaas/
http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
http://rna.urmc.rochester.edu/RNAstructureWeb/
http://www.targetscan.org/vert_72/
https://plantgrn.noble.org/psRNATarget/
http://meme-suite.org/