-- integrating multi-omics signatures via biological networks
Publications
Ewald J., Zhou, G., Lu, Y., Kolic, J., Ellis, C., Johnson, J.D., Macdonald P.E. and Xia, J. (2024)
"Web-based multi-omics integration using the Analyst software suite" Nature Protocols
(doi: 10.1038/s41596-023-00950-4)
Zhou, G., Pang Z., Lu, Y., Ewald, J. and Xia, J. (2022) "OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics"
Nucleic Acids Research (doi:10.1093/nar/gkac376).
Zhou, G. and Xia, J. (2018) "Using OmicsNet for Network Integration and 3D Visualization"
Current Protocols in Bioinformatics (doi:10.1002/cpbi.69).
Zhou, G. and Xia, J. (2018) "OmicsNet - a web-based tool for creation and visual analysis of biological networks in 3D space"
Nucleic Acids Research (doi:10.1093/nar/gky510).
Upload a list of mRNAs
Upload a list of proteins
You can copy and paste your list of significant feature (gene, metabolite etc) IDs
with optional associated p values or fold changes separated by tab. A small example data
is shown below (first column: Entrez ID, second column: fold change):
Coordinates format should in the form of [chr]:[start]-[end]:[strand]/[allele]. Some examples:
# SNP
5:140532-140532:1/C
# SNP (reverse strand)
14:19584687-19584687:-1/T
# insertion
1:881907-881906:1/C
# 5bp deletion
2:946507-946511:1/-
Upload a list transcription factors
Upload a Graph File
Upload and process peak list file
Upload a list of taxon names
You can copy and paste your list of significant taxon names
with optional associated abundance separated by tab. A small example data
is shown below (first column: Genus name, second column: abundance):
For taxon names, if there is a space (" ") in the name (i.e. unclassified Clostridiales) replace space with "_" (unclassified_Clostridiales).
If there are unclassified taxa in your data of the query taxonomy level, you can use the term “unclassified_” plus the parent taxonomy for estimation.
e.g.: f__Lachnospiraceae; g__; will be “unclassified_Lachnospiraceae” in the input box.
Confirmation
Are you sure about resetting? All currently uploaded data will be lost!
Supported file formats: .graphml, .sif, .json or .txt file containing edge list. For more information,
please read our FAQs or download example files below.
Supported formats: .csv or .txt, including four columns [m/z, RT, intensity and p value]. For more information,
please read our FAQs or download example files below.
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