1. TCGA 网页分析工具
文章 Website note Last updated R-index tutorial
GEOhttp://www.ncbi.nlm.nih.gov/geo GEO data set and simple analysis
c-Bioportalhttp://www.cbioportal.org/ TCGA,mutation,, CAN, Expression , Protein/protein phosphorylation
MERAVhttp://merav.wi.mit.edu/ analyze human gene expression across a large variety of arrays ；一个是分析基因在芯片中的表达，另一个是分析芯片中所有基因的表达。 数据可下载 ****** https://mp.weixin.qq.com/s/iKB_a5ncyroIvl1eWxg4Iw
Gepiahttp://gepia2.cancer-pku.cn/#general TCGA肿瘤数据综合分析，two gene correlation in cancer or pan cancer *****
Timerhttps://cistrome.shinyapps.io/timer/ TCGA肿瘤数据综合分析 *****
TCPAhttp://www.tcpaportal.org/tcpa/ TCGA肿瘤数据综合分析
linkedomics http://www.linkedomics.org/login.php 多组学TCGA数据分析
CRNhttp://syslab4.nchu.edu.tw/ mRNA, LnRNA, co-expression, cancer with stages, normal *****
networkanalyst https://www.networkanalyst.ca/ 分析TCGA, Arrayexress , GEO,导入自己的数据（***纯化数据，文本，不能有GEO的表头注释） *****
Survival Expresshttp://bioinformatica.mty.itesm.mx:8080/Biomatec/SurvivaX.jsp Survival analysis(single or multiple genes) *****
Cosmichttps://cancer.sanger.ac.uk/cosmic/ 癌症基因突变数据库
cell minerhttps://discover.nci.nih.gov/cellminer/loadDownload.do
oncolnchttp://www.oncolnc.org/ link TCGA survival data to mRNA, miRNA, or lncRNA expression levels ****
R2 Genomichttps://hgserver1.amc.nl/cgi-bin/r2/main.cgi analysis of GEO or TCGA data set，14万人表达数据 *****
ArrayExpresshttps://www.ebi.ac.uk/arrayexpress/
TCGA portalhttp://tumorsurvival.org/index.html gene survival, two gene correlation 2016/5/16 ****
Mexpresshttp://mexpress.be/ 甲基化与表达 ****
Mevhttp://mev.tm4.org cloud-based application supporting analysis, visualization, and stratification of large genomic data, particularly for RNASeq and microarray data of TCGA data and your data ***
genefriendshttps://www.networkanalyst.ca/ 表达分析与做图
oncominehttps://www.oncomine.org/resource/login.html ****
Genevestigatorlocal software for TCGA ****
GCBIhttps://www.gcbi.com.cn/gclib/html/gclibhome TCGA, GEO数据提取分析 *****
Tumor survival Pan cancer or TCGA ****
OncoLnchttp://www.oncolnc.org ****
http://ualcan.path.uab.edu/
其他网页工具
Website Web address keyword/functions 分类 推荐指数 paper linked
查自然基金http://www.letpub.com.cn/index.php?page=grant
查文献
Pubmedhttp://www.ncbi.nlm.nih.gov/pubmed
GCBIhttps://www.gcbi.com.cn/gclib/html/gclibhome NCBI文章分类
单基因信息库
NCBIhttp://www.ncbi.nlm.nih.gov 综合新网站 单基因信息库 *****
genecardshttp://www.genecards.org 了解基因的基本信息 单基因信息库 ****
Proteinaltashttp://www.proteinaltas.org 基因表达，蛋白表达 组织、细胞中的基因表达水平 单基因信息库 ***
pubmed reminerhttp://hgserver2.amc.nl/cgi-bin/miner/miner2.cgi 文献挖掘 单基因信息库 *****
Gopubmedhttp://www.gopubmed.com/web/gopubmed/） 文献挖掘 单基因信息库 ***
CCLE(cancer cell line Encyclopedia https://portals.broadinstitute.org/ccle/home 细胞系基因表达，可下载（https://software.broadinstitute.org/morpheus） 单基因信息库 ******
Des-ncRNA http://www.cbrc.kaust.edu.sa/des_ncrna/home/index.php human micro and long noncodingRNAs based on literature-mining 单基因信息库 **
GDSC http://www.cancerrxgene.org/ 肿瘤耐药研究 单基因信息库 **
UCSC Genome Browser http://genome.ucsc.edu/index.html 查找基因序列 及上下游序列 单基因信息库 ***** http://yuelab.org/Yue_slides.pdf
NAR数据库List http://www.oxfordjournals.org/our_journals/nar/database/c/ 挖掘神器的神器 *****
Array express http://www.ebi.ac.uk/arrayexpress/ 表达数据的简单分析与下载 表达数据 *****
GEO httoP://wwww.ncbi.nlm.nih.gov/geo 表达数据的简单分析与下载 *****
Morpheus https://software.broadinstitute.org/morpheus/ 表达数据的分析与下载(替代基因表达分析神器Gene-E, Heatmap, Clustring *****
Jaspr http://jaspr.genereg.net DNA序列预测TF binding site ****
转录调控相关
ENCODE transcrition Factor listhttps://www.encodeproject.org/search/?type=AntibodyLot&targets.investigated_as=transcription+factor ENCODE 用的TF, Histon Marker, RNA binding protein ****
RegulomeDBhttps://pubs.broadinstitute.org/mammals/haploreg/haploreg.php candidate regulatory SNPs at disease-associated loci.(SNP-> TF)
HaploReghttps://pubs.broadinstitute.org/mammals/haploreg/haploreg.php candidate regulatory SNPs at disease-associated loci.
AnimalTFDBhttp://bioinfo.life.hust.edu.cn/AnimalTFDB/#!/ 转录因子分离，聚类 *****
3D Genomehttp://promoter.bx.psu.edu/hi-c/ find cis regulator element, Hi-C *****
Cistromemaphttp://cistrome.org/db/#/ ****, 收录了14000多套人和小鼠的ChIP-seq数据，包含800多个转录因子（简称TF) 转录调控相关 ******
UCSC Genome Browserhttp://genome.ucsc.edu/index.html chromosome view 转录调控相关 *****
ENCODEhttp://genome.ucsc.edu/ENCODE/index.html epiegenetic data, Ch-Ip 转录调控相关 ****
factorbookhttp://www.factorbook.org/human/chipseq/tf/ 数据没有cistromer全，但是 分类浏览TF。您可以选择您关注的功能或结构类型，看看这一类型的TF在哪些细胞里有ChIP-seq数据。同时它还整合了组蛋白修饰数据和核小体定位数据，查看该TF附近的组蛋白修饰和核小体分布 转录调控相关 ***
Cistromemap toolskithttp://dbtoolkit.cistrome.org/ TF-> Target, Target-> TF, DNA-> TF, TF-> TF 转录调控相关 *****
BETAhttp://cistrome.org/BETA/ TF-> Target, Target-> TF, DNA-> TF, TF-> TF 转录调控相关
BETA onlinehttp://cistrome.org/ap/root
Bird Big Datahttps://github.com/WeiqiangZhou/BIRD. RNA表达数据-》encode/cistrome->TF预测， transcriptome to predict its genome-wide 29 regulatory element activities 转录调控相关 ***** https://www.ncbi.nlm.nih.gov/pubmed/29051481
RPI-seq 预测RNA（LncRNA)和蛋白的相互作用 表观遗传
http://www.roadmapepigenomics.org/ epigenetic PI, Protocl et al,美国NIH资助的表观组学线图计划
STAR http://tabit.ucsd.edu/sdec/login.php
ENCODE https://www.encodeproject.org/ Encode data, protocol *******
WashU EpiGenomeBrowser http://epigenomegateway.wustl.edu/
其他工具
MultiGPShttp://mahonylab.org/software/multigps/ compare Ch-ip data cross samples
qphoshttp://qphos.cancerbio.info/index.php 蛋白磷酸化位点search
tools
RNA foldinghttp://rna.urmc.rochester.edu/RNAstructureWeb/ 预测RNA二级结构 tools
Circbasehttp://www.circbase.org/ cirRNA 序列调取 tools
Davidhttps://david.ncifcrf.gov 基因功能注释， KOBAS KEGG
venn图制作： "http://bioinfogp.cnb.csic.es/tools/venny/index.html
在线venn图制作："http://bioinformatics.psb.ugent.be/webtools/Venn/
GSEA analysishttp://www.webgestalt.org/2019/ ****
GTExhttps://www.gtexportal.org/home/ 正常组织，基因表达， SNP, eQTL, PCR,Historogy… ******
https://jhubiostatistics.shinyapps.io/recount/
biojupieshttps://amp.pharm.mssm.edu/biojupies/ online RNA-seq anlysisi for your data, public data(GEO, GTEx..) ****
chip-seq analysis galaxyhttp://cistrome.org/ap/root/index
http://www.tfmapper.org/ seq/DNase-seq数据预测感兴趣基因的调控因子
protein methylationpredicthttp://bioinfo.icgeb.res.in/PRmePRed/Protein sumolation predict` http://sumosp.biocuckoo.org/online.php
http://www.tfmapper.org/ seq/DNase-seq数据预测感兴趣基因的调控因子
Biogps http://biogps.org/#goto=welcome **** 基因组织分布， 数据库基因表达）
TCGA的DNA甲基化与表达数据的工具——MEXPRES https://mexpress.be/ ***
GEO analysis神器 GeoDiver(https://www.geodiver.co.uk/ ****
CHIP data http://chip-atlas.org/
Cancer metabolism gene network https://bioinfo.uth.edu/ccmGDB/index.html?csrt=6192416331046699915
Web, ORA, GSEA, network analysis, used by Linkedomics http://www.webgestalt.org/ *****
Enricher http://amp.pharm.mssm.edu/Enrichr/
online scRNAseq analysis http://granatum.dcmb.med.umich.edu:8102/?state_id=7b24da7fdf92ec5d&tab=info ***
G: profiler http://biit.cs.ut.ee/gprofiler/gost **** 富集分析， ID转换
predit protein interaction network http://www.chilibot.net
Biogrind https://thebiogrid.org/ 蛋白相互作用
clinical trial https://www.clinicaltrials.gov/