When the run is finished, a notice email will be sent to you. Wait for job submitting.
Gene-Network-Builder
Documentation
Project info
Project Name
Email
Binding sites
Transciption Factor
Gene symbol of the TF
ChIP results
List of gene symbols seperated by ';' OR
Upload a text file
Expression Data
Gene expression results
A matrix in
this format
or a text file with gene symbols
miRNAs expression profile
Optional. CSV file with
specific format
FoldChange>=
Fold change cutoff for gene expression results
P.Value=<
p.value cutoff for gene expression results
Resolve genes with multiple expression measurements
use maximum
use median
use minimum
Please select a method for determining the fold change of gene with multiple probes
Network options
Protein-DNA Interactions (PDIs)
EDGEdb, microCosm, C.elegans
EDGEdb, C.elegans
TFBF, WeiNiu et.al., C.elegans
modEncode ChIP, C.elegans
modEncode, Embryo, C.elegans
modEncode, late Embryo, C.elegans
modEncode, starved, C.elegans
modEncode, L1, C.elegans
modEncode, L2, C.elegans
modEncode, L3, C.elegans
modEncode, L4, C.elegans
modEncode, L4-Young Adult, C.elegans
modEncode, Young Adult, C.elegans
All PDI from Y1H & ChIP, C.elegans
Predict-interactions for C.elegans
modEncode, microCosm, D.melanogaster
modEncode, Adult_Female, D.melanogaster
modEncode, Adult_Male, D.melanogaster
modEncode, Embryo, D.melanogaster
modEncode, L1, D.melanogaster
modEncode, L2, D.melanogaster
modEncode, L3, D.melanogaster
modEncode, Pupae, D.melanogaster
modEncode, WPP, D.melanogaster
flyBase, D.melanogaster
Fantom4, Encode and miRgen, H.sapiens
yeastract, S.cerevisiae
IyerLab, S.cerevisiae
Upload PDIs
PDIs file is a windows comma separated value (csv) file. It is a from-to 2 column file. Click
here
to download the sample file.
OR
upload a customized PDIs
Depth of output network
Expand the gene list from the ChIP results with the selected PDIs
Tolerance
0 unverified node per path
1 unverified node per path
Maximum number of nodes without expresion change detected in each path allowed
Do not keep miRNA if absent in the ChIP results or expression results
All the leaf nodes should be verified by expression results
Only keep the best path if multiple paths exist for a node
Include GO analysis
