iSeq is a websever to help you analyse RNA sequencing data and plot publishable figures.

Upload your genes Expression data first !

If iSeq is new to you, look this: workflow, tutorial

                    
iSeq @ Bioinformatics core facility, Center for Life Science, Peking University

Condition:

Expression:

Download the data.

Upload Your Data First !

Normalization is a key step in RNA-seq data analysis.

Box plot:

hclust

Expression Distribution:

Clust heatmap

MA plot: (Just using the first 2 samples)

Upload Your Data First !

Optional filter:

Download Table
Detect differentially expressed genes using DESeq.
Anders S and Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, pp. R106



Upload Your Data First !

Download Table
Detect differentially expresed genes using expression fold change.





Several highly recommended online gene functional enrichment tools are list below, you can copy the DEGs to clipboard and submit them to these tools.

David

DAVID provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.


Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009;4(1):44-57.
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1-13.


Enrichr

Enrichr is an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis


Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;128(14).
Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377.
Gene Ontology enrichment using DAVID webserver
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009;4(1):44-57.
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1-13.


KEGG pathway enrichment using DAVID webserver
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009;4(1):44-57.
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1-13.


Download Table
Gene Ontology enrichment using GOseq.
Young MD, Wakefield MJ, Smyth GK and Oshlack A (2010). “Gene ontology analysis for RNA-seq: accounting for selection bias.” Genome Biology, 11, pp. R14


Gene Expression bar plot:

Gene List (DEGs by default):


Heatmap:

Principal Components Analysis:

T-Distributed Stochastic Neighbor Embedding(t-SNE)):

Warning: t-SNE suits for large number of samples. If your sample number < 10, we highly recommend you using PCA.

About

iSeq is a web-based platform for RNA-seq research. If you are new to iSeq read the tutorial (English version, Chinese version).

                    


The iSeq is designed and supported by bioinformatics core facility @ Peking University.
This is a free, public, internet accessible resource. Data transfer and data storage are not encrypted. If you worry about the security of data, you are encouraged to setup your own local iSeq on your computer.
Github page: https://github.com/Czh3/iSeq



Any bugs or suggestion report to Czh3 (Email: zhangchao3@hotmail.com).