Ortho2ExpressMatrix - a web server that interprets cross-species gene expression data by gene family information   Ortho2ExpressMatrix - a web server that interprets cross-species gene expression data by gene family information

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Ortho2ExpressMatrix is a Web Server that provides combined information on gene expression and gene families of two objects for the user's (external) gene expression data to be associated with (internal) gene family information from the tool's data background.

Some short features:
  • Objects can be organisms (species: Hs, Mm, Ce, Dm, Sc), individuals, cell lines, tissues, or two techniques for an identical biological individual.
  • Data annotation can be on gene, transcript, protein level or given by probe set annotation. Annotation levels can be mixed for the two objects but must be applied either for either protein coding genes or for microRNAs.
  • Supported expression data types: Either gene expression data (ratios to be calculated) or differential gene expression (given ratios, log2-ratios, log10-ratios) can be uploaded from one or two files. Ortho2ExpressMatrix processes currently no mixed data types.
  • Supported data formats: tab separated plain text files; users can directly upload GEO Series files; EXCEL file tables must be converted to *.txt format.
  • Ortho2ExpressMatrix visualizes genomic, proteomic or transcriptomic expression data of protein coding genes with respect to one out of four protein family approaches; or, microRNA expression data to one out of two microRNA family approaches.
  • The idea in Ortho2ExpressMatrix is to filter out those paralogous genes that react in a similar way (by differential gene expression) on a disturbance of the cell, e.g., a disease, a gene knock-out, etc.
Helps are given in the USAGE section. Some information on data in the background are given in the FAQs section. Test visualizations can be directly carried out below for test data files that contain random data.
Test data are randomized for display information purposes only. Have a look on the output visualization (press button) as well as on the input data format of the test data files (follow link).
Start example directly for randomized protein coding gene expression data. Hints for usage and settings to reproduce the test output are given here - download test data file
Start example directly for randomized microRNA expression data. Hints for usage and settings to reproduce the test output are given here - download test data file
Data configuration and data upload from the user's file space
1. annotation data gene annotation feature used in the data file: probe level ⇒ transcript level ⇒ protein level || gene level
A. Ensembl version
49 53 59 63
B. annotation level for organism 1
B. annotation level for organism 2
gene Select this if Ensembl gene identifier, e.g. ENSG00000000001, is associated to your data. Confirm and select organism in C. transcript Select this if Ensembl transcript identifier, e.g. ENST00000000001, annotation is associated to your data. Confirm and select organism in C. protein Select this if Ensembl protein identifier, e.g. ENSP00000000001, is associated to your data. Confirm and select organism in C. miRNA Select this if miRBase annotation for mature microRNAs, e.g. hsa-miR-31, is associated to your data. Confirm and select organism in C. probe level Select this if probe annotation is in your data. Confirm and select microarray platform in C.  
gene Select this if Ensembl gene identifier, e.g. ENSG00000000001, is associated to your data. Confirm and select organism in C. transcript Select this if Ensembl transcript identifier, e.g. ENST00000000001, annotation is associated to your data. Confirm and select organism in C. protein Select this if Ensembl protein identifier, e.g. ENSP00000000001, is associated to your data. Confirm and select organism in C. miRNA Select this if miRBase annotation for mature microRNAs, e.g. hsa-miR-31, is associated to your data. Confirm and select organism in C. probe level Select this if probe annotation is in your data. Confirm and select microarray platform in C.
C. platform / organism of 1
C. platform / organism of 2
HELP for this section
 
2. expression data data from one or two files and four data columns: gene annotation feature ⇒ expression values (alternative A)
 
Load data file for organism 1
Define annotation and value columns
annotation, col. file 1, organism 1 - treatment, col. file 1, organism 1 - control, col. download test data file
Load data file for organism 2
Define annotation and value columns
annotation, col. file 2, organism 2 - treatment, col. file 2, organism 2 - control, col.  
HELP for this section
 
Family level to be defined: Protein or gene family approach
Select a protein family approach
EnsemblCompara Orthology/Paralogy InParanoid7 SYSTERS4 Ensembl Family
Select a microRNA family approach
miRBase 16 TargetScan 5.1
HELP for this section
 
Restrict to single groups/families/clusters or single proteins/genes
Pre-select group/family/cluster
due to the family approach
Exclude singleton families
show all exclude single protein families exclude single gene families (families of genes without any given expression are always excluded)
Pre-select gene (by gene name,
Ensembl gene ID, or protein ID)

ENSG00000159216 - ENSP00000340690 - RUNX1 (or respective annotation of other organisms; case sensitive)
HELP for this section
 
Output configuration
Filter and indicate
as checked HTML box
no indication all parallel-regulated all parallel-up-regulated only all parallel-down-regulated only all anti-parallel-regulated
Define significance criterion (default ratio: 3/4 - 4/3; change the lower ratio threshold only, the upper threshold is the reciprocal ratio, automatically; use decimal numbers; fold change of 2 is: 1 / 2 = 0.5)
Output as matrix
matrices with significant values only all matrices
HELP for this section
 
Output as table
table with significant values only full table (not regarding significance and pre-selection criteria, but regarding family type exclusion)
HELP for this section
 
Perform query