ImmuNet protocols

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ImmuNet specifications

Information


Unique identifier OMICS_23341
Name ImmuNet
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Olga G. Troyanskaya <>
  • person_outline Stuart Sealfon <>

Additional information


http://immunet.princeton.edu/about/ http://immunet.princeton.edu/predictions/gene/tutorial/?network=antigen_processing_and_presentation&gene=18657

Publication for ImmuNet

ImmuNet in pipeline

2017
PMCID: 5266700
PMID: 28184219
DOI: 10.3389/fmicb.2017.00082

[…] phages were selected from each library for dna sequencing (genscript, nanjing, china); the obtained sequences were analyzed as follows. first, mimotopes were searched in the sarotup database (http://immunet.cn/sarotup) to exclude target-unrelated peptides (tups; huang et al., ). the clustal omega program (http://www.ebi.ac.uk/tools/msa/clustalo/) was used for multiple-sequence alignment […]


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ImmuNet in publications

 (16)
PMCID: 5834250
PMID: 29541392
DOI: 10.18632/oncotarget.24228

[…] tumors []. several complement system-related functional annotations (table ) are also shared between tcga m0214 and brain m0257. in addition, rnase6, one of the 22 matching genes, was searched with immunet, a regulatory network database for immune system-related genes []. at a confidence level > 99%, eight of the other 21 genes shared a function with rnase6 in the complement system ()., […]

PMCID: 5849184
PMID: 29560120
DOI: 10.18632/oncotarget.24161

[…] regulator for immune response processes (figure ). to evaluate the reproducibility, we also compiled a list of 796 genes as immu_genes from 15 expert-curated kegg immune-related pathways (http://immunet.princeton.edu./) [] (). the results were highly concordant across the two lists of immu_genes from different sources, which independently validated the strong negative correlation […]

PMCID: 5653836
PMID: 29062084
DOI: 10.1038/s41598-017-14195-1

[…] to the ph.d.tm-c7c kit instructions. after sequencing and inference of amino acid sequences by gene runner version 5.0, the peptides were analysed in the biopanning data bank (mimodb) (http://immunet.cn/bdb/) to discard target-unrelated peptides. based on default parameters for the blastp (score ≥18.5), the selected peptides were blasted against the refseq_protein database for the homo […]

PMCID: 5593188
PMID: 28892521
DOI: 10.1371/journal.pone.0183969

[…] extracted and sequenced according to ph.d.-c7c kit instructions. the amino acid sequences were deduced with gene runner program version 5.0 and checked in the biopanning data bank (mimodb) (http://immunet.cn/bdb/) []. the selected peptides were blasted for homo sapiens proteins, using the blastp tool and refseq protein database []., among proteins deduced from the detected peptides, proteins […]

PMCID: 5870750
PMID: 28881994
DOI: 10.1093/bioinformatics/btx260

[…] genes within each gene set. the kegg network incorporated pathway topology and was built using the kegggraph r package v1.26.0 (). immuneglobal and exponly_immuneglobal networks were obtained from immunet and edges were restricted to those with confidence of at least 0.1 (). the string network incorporated all experimental evidence from the string database v10.0. the processed lincs l1000 gene […]


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ImmuNet institution(s)
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; New York Genome Center, New York, NY, USA; Simons Center for Data Analysis, Simons Foundation, New York, NY, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Departments of Pathology and Immunobiology, Yale School of Medicine, New Haven, CT, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA
ImmuNet funding source(s)
Supported by NIH Contract HHSN272201000054C and Grant 1U19AI117873; by a Senior Fellow of CIFAR and by T32 MH096678.

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