bioWebtree

This a web tools list for zhang lab used.

The web tree list consists of frequently used websites for genes. This tree contains three aspects of genes: Genome, Protein and Fuction.

This is just part of the summary. If you have more supplement websites that you want to add into bioWebtree. Please edit README.md file.

bioWebtree overview

Genome

Sequence

UCSC https://genome.ucsc.edu/

• Chromosome tracker (Gene — position)
• DNA sequence (Gene name, Chr position)

Ensembl https://asia.ensembl.org/

• DNA sequence (Gene name)
• Exon, intron, transcript variant

Mutation

TCGA-GDC https://portal.gdc.cancer.gov/

• Cancer mutation
• Impact Categories

• Only TCGA

COMICS https://cancer.sanger.ac.uk/cosmic

• Mutations, CNV
• Cell lines mutations
• Lager datasets

Expression

CCLE https://portals.broadinstitute.org/ccle

• Gene expression in cell lines
• Cell lines mutations

• Note: Registration required

TISSUE https://tissues.jensenlab.org/

• Gene expression in normal tissues
• Multiple species (Human, mice…)

• Relative expression

GTEx https://www.gtexportal.org/

• Gene expression in normal tissues
• Beautiful plots

• Only in human

Xena https://xenabrowser.net/

• Expression comparsion (normal vs tumor, tumor stages, tumor subtypes)
• Correlation between two genes
• Survival plot
• User defined dataset

• Only one cancer type can be viewed at a time

cBioportal http://www.cbioportal.org/

• Expression comparsion (tumor stages, tumor subtypes)
• Correlation between genes (1 vs mutiple genes)
• Mutation and CNV
• Multiple datasets

• No normal data

oncomine https://www.oncomine.org/

• Expression comparsion (normal vs tumor)
• Multiple datasets (GEO, TCGA)
• Overview

• Does not support download
• Note: Registration required

GEPIA2 http://gepia2.cancer-pku.cn/

• Expression comparsion in pancancer (normal vs tumor)
• Correlation between genes
• Survival, most differential survival genes

corpan http://sc-brca.cn/corpan/

• Correlation between two genes in pancancer

Protein

Sequence

Domain

UniProt https://www.uniprot.org/

• Overviews about protein
• download Fasta form
• Blast protein sequence

Modification

GPS http://gps.biocuckoo.cn/

• Predict protien post-translation modifications(site/enzyme)
• online Illustrate
• Database (PTM/autophagy/phase separation/etal)

PhosphoSitePlus https://www.phosphosite.org/homeAction

• High/low Throughput sites

Location

Human Protein Atlas http://www.proteinatlas.org/

• tissue expression/cell sublocation
• IF image

Functions

Already Known

GeneCards https://www.genecards.org

• most comprehensive resource to know a new gene