Tag: Human

NetGene 2.42 – Intron Splice Sites in Human, C. Elegans & A. Thaliana DNA

NetGene 2.42

:: DESCRIPTION

NetGene2 is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetGene2 Source Code

:: MORE INFORMATION

Citation

S.M. Hebsgaard, P.G. Korning, N. Tolstrup, J. Engelbrecht, P. Rouze, S. Brunak
Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information
Nucleic Acids Research, 1996, Vol. 24, No. 17, 3439-3452.

Brunak, S., Engelbrecht, J., and Knudsen, S.
Prediction of Human mRNA Donor and Acceptor Sites from the DNA Sequence
Journal of Molecular Biology, 1991, 220, 49-65.

LocFuse – Human protein-protein Interaction Prediction

LocFuse

:: DESCRIPTION

LocFuse is a novel ensemble learning method of human protein-protein interaction prediction via classifier fusion using protein localization information.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 LocFuse

:: MORE INFORMATION

Citation

LocFuse: human protein-protein interaction prediction via classifier fusion using protein localization information.
Zahiri J, Mohammad-Noori M, Ebrahimpour R, Saadat S, Bozorgmehr JH, Goldberg T, Masoudi-Nejad A.
Genomics. 2014 Dec;104(6 Pt B):496-503. doi: 10.1016/j.ygeno.2014.10.006.

CanProVar 2.0 – Human Cancer Proteome Variation Database

CanProVar 2.0

:: DESCRIPTION

CanProVar is designed to store and display single amino acid alterations including both germline and somatic variations in the human proteome, especially those related to the genesis or development of human cancer based on the published literatures.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.
Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B, Li Y, Li J.
J Proteome Res. 2017 Feb 3;16(2):421-432. doi: 10.1021/acs.jproteome.6b00505.

SPIKE – Database of highly curated human Signaling Pathways

SPIKE

:: DESCRIPTION

SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database of highly curated human signaling pathways with an associated interactive software tool.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

SPIKE: a database of highly curated human signaling pathways.
Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R.
Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9. doi: 10.1093/nar/gkq1167.

GAPI – Explores Hyperbolic Mapping of the human Potein Interaction Network

GAPI

:: DESCRIPTION

GAPI (Geometric Analysis of the Protein Interactome) is a web tool for the geometric analysis of the hPIN.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Aug 15;34(16):2826-2834. doi: 10.1093/bioinformatics/bty206.
The latent geometry of the human protein interaction network.
Alanis-Lobato G, Mier P1,2, Andrade-Navarro M.

HIPPIE 2.2 – study and filter the Network of Human Protein-protein Interaction data

HIPPIE 2.2

:: DESCRIPTION

HIPPIE (Human Integrated Protein-Protein Interaction rEference) is a human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 HIPPIE

:: MORE INFORMATION

Citation

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks.
Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH.
Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414. doi: 10.1093/nar/gkw985

PLoS One. 2012;7(2):e31826. doi: 10.1371/journal.pone.0031826. Epub 2012 Feb 14.
HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH1, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.

GWAB – Web Server for Network-based Boosting of Human Genome-wide Association data

GWAB

:: DESCRIPTION

GWAB (genome-wide Association Boosting) is a web server for the network-based boosting of human GWAS data.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2017 Jul 3;45(W1):W154-W161. doi: 10.1093/nar/gkx284.
GWAB: a web server for the network-based boosting of human genome-wide association data.
Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I.

TRRUST v2 – Curated TF-target Interaction Networks in Human and Mouse

TRRUST v2

:: DESCRIPTION

TRRUST (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining) is a manually curated database of human and mouse transcriptional regulatory networks.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions.
Han H, et al.
Nucleic Acids Res. 2018 Jan 4;46(D1):D380-D386. doi: 10.1093/nar/gkx1013.

HumanNet v2 – Human Gene Networks for Disease Research

HumanNet v2

:: DESCRIPTION

HumanNet is a human functional gene network by integrating diverse types of omics data using Bayesian statistics framework and demonstrated its ability to retrieve disease genes.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

HumanNet v2: human gene networks for disease research.
Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I.
Nucleic Acids Res. 2019 Jan 8;47(D1):D573-D580. doi: 10.1093/nar/gky1126.

MORPHIN – Model Organisms Projected on a Human Integrated Gene Network

MORPHIN

:: DESCRIPTION

MORPHIN is a web-based bioinformatics tool to study human diseases using model organism genes.

::DEVELOPER

Network Biomedicine Laboratory  at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.
Hwang S, Kim E, Yang S, Marcotte EM, Lee I.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W147-53. doi: 10.1093/nar/gku434.