Microarray

Please enter a short name for your analysis.:

Microarray Data Import

Select data import option.

Input Type:

onlineimport

celfiles

procdata

Please enter the NCBI GEO accession number for the dataset. We support GSE and GDS datasets, so accession must start from GSE or GDS e.g. GSE14407 or GDS3592.:

Upload a Zip file:

Please upload zip file containing all the celfiles.

Please select data normalisation method.:

Please upload a file containing processed data. File must be in a csv format with headers. Format - first row=probes then columns=samples.

Select chip type:

Upload sample annotation file:

Please upload a sample annotation file. File must be in csv format with column headers. First column name must be sample names as in the data file and second column name must be the condition (like normal/cancer etc).

Select top genes (optional)

Select top genes using either highest average expression or maximum coefficient of variation of genes across all samples.

Please select the selectGenesMethod for selecting top genes in the dataset.

Differential Gene Expression Analysis

Perform differential gene expression data analysis.

Please select differential gene expression detection method.:

Analysis of differentially expressed genes (optional)

Perform trend analysis using JT test - Jonckheere-Terpstra test.

Regulatory Impact Factors (RIF) Analysis

Signalling Pathway Impact Analysis

Broad gene set analysis.

Select the geneset for Broad geneset analysis.:

Cancer Outlier Profile Analysis (COPA).

modified Cancer Outlier Profile Analysis (mCOPA)

Select percentile value for mCOPA.:

Gene regulatory network inference.

Please select GRN inference method.:

Compare feature selection and clustering methods.

Gene-list Analysis Framework

Functional enrichmnent analysis using DAVID

Druggability analysis using CancerResource

Functional annotation of genes using gProfileR

Functional annotation of genes using EDanalysis

Gene Enrichment Disequilibrium Analysis using EDanalysis for BP

Gene Enrichment Disequilibrium Analysis using EDanalysis for MF

Gene Enrichment Disequilibrium Analysis using EDanalysis for CC

Promoter analysis

Select the upstream region:

Select the downstream region:

Extract the promoter sequences for the input genes

Detect CpG islands in the promoter sequences of the input genes

Remove sequences with over GC content in the promoter sequences of the input genes. (>55% GC content for human)

Submit the input genes to MEME Suite of tools for Motif Discovery, Motif Comparison and Motif Enrichment Analysis

Perform TFBS over-representation analysis using oPOSSUM

INsPeCT

Links

Microarray