Tag: Human

Netview – Explore the Human and Mouse Gene Regulatory Networks

Netview

:: DESCRIPTION

Netview is a free web tool that allow end users to explore the human and mouse gene regulatory networks. Users can query the system by providing a gene identifier and the boundaries of the subnetwork being explored. The system provides the list of interactions, the enriched Gene Ontology Terms together with a graphical representation of the subnetwork.

::DEVELOPER

di Bernardo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1101:179-96. doi: 10.1007/978-1-62703-721-1_10.
Reverse engineering transcriptional gene networks.
Belcastro V, di Bernardo D.

PROmiRNA v2 – Annotating miRNA Promoters in Human

PROmiRNA v2

:: DESCRIPTION

PROmiRNA is a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features.

::DEVELOPER

PROmiRNA team , Max Planck Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Python

:: DOWNLOAD

 PROmiRNA

:: MORE INFORMATION

Citation

Genome Biol. 2013 Aug 16;14(8):R84. [Epub ahead of print]
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.
Marsico A1, Huska MR, Lasserre J, Hu H, Vucicevic D, Musahl A, Orom UA, Vingron M.

GenCLiP 3 – Human Gene Function And Network Analysis

GenCLiP 3

:: DESCRIPTION

GenCLiP is a literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. GenCLiP can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.

::DEVELOPER

GenCLiP team

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wang JH, Zhao LF, Wang HF, Wen YT, Jiang KK, Mao XM, Zhou ZY, Yao KT, Geng QS, Guo D, Huang ZX.
GenCLiP 3: mining human genes’ functions and regulatory networks from PubMed based on co-occurrences and natural language processing.
Bioinformatics. 2019 Nov 4:btz807. doi: 10.1093/bioinformatics/btz807. Epub ahead of print. PMID: 31681951.

Bioinformatics. 2014 Apr 23. pii: btu241. [Epub ahead of print]
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms.
Wang JH, Zhao LF, Lin P, Su XR, Chen SJ, Huang LQ, Wang HF, Zhang H, Hu ZF, Yao KT, Huang ZX.

BMC Bioinformatics. 2008 Jul 13;9:308.
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords.
Huang ZX, Tian HY, Hu ZF, Zhou YB, Zhao J, Yao KT.

HPMV – Human (Protein) Mutation Viewer

HPMV

:: DESCRIPTION

HPMV: Human (Protein)  Mutation Viewer

::DEVELOPER

the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

hmv

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 HPMV

:: MORE INFORMATION

Citation

Sherman WA, Kuchibhatla DB, Limviphuvadh V, Maurer-Stroh S, Eisenhaber B, Eisenhaber F.
HPMV: human protein mutation viewer – relating sequence mutations to protein sequence architecture and function changes.
J Bioinform Comput Biol. 2015 Oct;13(5):1550028. doi: 10.1142/S0219720015500286. Epub 2015 Oct 27. PMID: 26503432.

polyadq – Detection of Human Polyadenylation Signals

polyadq

:: DESCRIPTION

polyadq is a program for detection of human polyadenylation signals. To avoid training on possibly flawed data, the development of polyadq began with a de novo characterization of human mRNA 3′ processing signals. This information was used in training two quadratic discriminant functions that polyadq uses to evaluate potential polyA signals.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Gene. 1999 Apr 29;231(1-2):77-86.
Detection of polyadenylation signals in human DNA sequences.
Tabaska JE, Zhang MQ.

FirstEF – Human First Exon Finder

FirstEF

:: DESCRIPTION

FirstEF (First Exon Finder) is a 5′ terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential first donor sites and CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first donor site (GT) and an upstream promoter region, FirstEF decides whether or not the intermediate region can be a potential first exon, based on a set of quadratic discriminant functions.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Computational identification of promoters and first exons in the human genome.
Davuluri RV, Grosse I, Zhang MQ.
Nat Genet. 2001 Dec;29(4):412-7. Erratum in: Nat Genet 2002 Nov;32(3):459.

CNVannotator 20131114 – Annotation Server for Copy Number Variation (CNV) in Humans

CNVannotator 20131114

:: DESCRIPTION

CNVannotator is a web server that accepts an input set of human genomic positions in a user-friendly tabular format.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory,

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2013 Nov 14;8(11):e80170. doi: 10.1371/journal.pone.0080170. eCollection 2013.
CNVannotator: a comprehensive annotation server for copy number variation in the human genome.
Zhao M1, Zhao Z.

PhenoPred – Detect novel Gene-disease Associations in Humans

PhenoPred

:: DESCRIPTION

PhenoPred is a web-based tool designed to detect novel gene-disease associations in humans. It is based on known gene-disease associations, protein-protein interaction data, protein functional annotation at a molecular level and protein sequence data. Machine learning principles are used to integrate heterogeneous data sources. PhenoPred can be used to prioritize genes based on their likelihood to be associated with a given disease or to prioritize diseases for a given query gene.

::DEVELOPER

PhenoPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Proteins. 2008 Aug 15;72(3):1030-7. doi: 10.1002/prot.21989.
An integrated approach to inferring gene-disease associations in humans.
Radivojac P1, Peng K, Clark WT, Peters BJ, Mohan A, Boyle SM, Mooney SD.

GlycoMine – Predicting N-, C- and O-linked glycosylation in the Human Proteome

GlycoMine

:: DESCRIPTION

GlycoMine is a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome

::DEVELOPER

Jiangning Song, Ph.D.

:: SCREENSHOTS

GlycoMine

:: REQUIREMENTS

  • Linux/MacOsX/ Windows
  • Java

:: DOWNLOAD

 GlycoMine

:: MORE INFORMATION

Citation:

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.
Li F, Li C, Wang M, Webb GI, Zhang Y, Whisstock JC, Song J.
Bioinformatics. 2015 Jan 6. pii: btu852.

HTJoinSolver 0.4A – Human Immunoglobulin VDJ Partitioning

HTJoinSolver 0.4A

:: DESCRIPTION

HTJoinSolver is a pubically available application to assist researchers in partitioning the V(D)J regions of immunogloblulin.

::DEVELOPER

the Office of Intramural Research, Center for Information Technology in collaboration with the Vaccine Research Center at the National Institute of Allergy and Infectious Diseases.

:: SCREENSHOTS

HTJoinSolver

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 HTJoinSolver

:: MORE INFORMATION

Citation

HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs.
Russ DE, Ho KY, Longo NS.
BMC Bioinformatics. 2015 May 23;16(1):170. doi: 10.1186/s12859-015-0589-x.