Tag: Human

miRTarBase 8.0 – microRNA-target Interactions database

miRTarBase 8.0

:: DESCRIPTION

As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.

::DEVELOPER

Integrative System Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Jul 26;12:300. doi: 10.1186/1471-2105-12-300.
miRTar: an integrated system for identifying miRNA-target interactions in human.
Hsu JB, Chiu CM, Hsu SD, Huang WY, Chien CH, Lee TY, Huang HD.

Nucleic Acids Res. 2011 Jan;39(Database issue):D163-9. doi: 10.1093/nar/gkq1107.
miRTarBase: a database curates experimentally validated microRNA-target interactions.
Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD.

RefLnc – comprehensive Annotation for human long noncoding RNAs(lncRNAs)

RefLnc

:: DESCRIPTION

RefLnc is a comprehensive annotation for human long noncoding RNAs(lncRNAs).Each lncRNA in the atlas is characterized by a panorama of sequence, expression and trait association.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • R

:: DOWNLOAD

RefLnc

:: MORE INFORMATION

Citation

Jiang S, Cheng SJ, Ren LC, Wang Q, Kang YJ, Ding Y, Hou M, Yang XX, Lin Y, Liang N, Gao G.
An expanded landscape of human long noncoding RNA.
Nucleic Acids Res. 2019 Sep 5;47(15):7842-7856. doi: 10.1093/nar/gkz621. PMID: 31350901; PMCID: PMC6735957.

AnnoLnc 2.1 – Annotate human lncRNAs

AnnoLnc 2.1

:: DESCRIPTION

AnnoLnc2 is a web server to provide on-the-fly analysis for novel human or mouse lncRNAs.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

AnnoLnc

:: MORE INFORMATION

Citation

Ke L, Yang DC, Wang Y, Ding Y, Gao G.
AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse.
Nucleic Acids Res. 2020 Jul 2;48(W1):W230-W238. doi: 10.1093/nar/gkaa368. PMID: 32406920; PMCID: PMC7319567.

CADD 1.6 – Estimating the Relative Pathogenicity of human Genetic Variants

CADD 1.6

:: DESCRIPTION

CADD (Combined Annotation Dependent Depletion) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CADD

 :: MORE INFORMATION

Citation

Nat Genet. 2014 Mar;46(3):310-5. doi: 10.1038/ng.2892. Epub 2014 Feb 2.
A general framework for estimating the relative pathogenicity of human genetic variants.
Kircher M1, Witten DM2, Jain P3, O’Roak BJ1, Cooper GM4, Shendure J5.

LocusExplorer 0.7.2 – Visualisation of Human Genetic Association data and Biological Annotations

LocusExplorer 0.7.2

:: DESCRIPTION

LocusExplorer is a data visualisation and exploration tool for genetic association data.

::DEVELOPER

The Oncogenetics Team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 LocusExplorer

:: MORE INFORMATION

Citation

LocusExplorer: a user-friendly tool for integrated visualisation of human genetic association data and biological annotations.
Dadaev T, Leongamornlert DA, Saunders EJ, Eeles R, Kote-Jarai Z.
Bioinformatics. 2015 Nov 20. pii: btv690.

DASHR – Database of small human noncoding RNAs

DASHR

:: DESCRIPTION

The DASHR database provides information about small non-coding RNA (sncRNA) and their expression in different human tissues and cell types. The content of this database derives from curation, annotation, and computational analysis of small RNA sequencing data sets from multiple sources. Currently the database contains information about more than 46,000 sncRNAs in 42 normal human tissues and cell types from over 30 independent studies.

::DEVELOPER

 Wang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, and Li-San Wang.
DASHR: database of small human noncoding RNAs.
Nucl. Acids Res., 2015 (Database Issue) doi:10.1093/nar/gkv1188

PIPs 1.1 – Human Protein-Protein Interaction Predictions

PIPs 1.1

:: DESCRIPTION

PIPs is a database of predicted human protein-protein interactions. The predictions have been made using a na?ve Bayesian classifier to calculate a Score of interaction.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

 NO

:: MORE INFORMATION

Citation

PIPs: human protein–protein interaction prediction database
Mark D. McDowall, Michelle S. Scott and Geoffrey J. Barton
Nucl. Acids Res. (2009) 37 (suppl 1): D651-D656. doi: 10.1093/nar/gkn870

LR_PPI – large-scale Prediction of Human protein-protein interaction

LR_PPI

:: DESCRIPTION

LR_PPI is a web server for large-scale prediction of human protein-protein interaction from amino acid sequence based on latent topic feature

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Proteome Res. 2010 Oct 1;9(10):4992-5001. doi: 10.1021/pr100618t.
Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features.
Pan XY1, Zhang YN, Shen HB.

iLocator – An Image-based Multi-label Human Protein Subcellular Localization Predictor

iLocator

:: DESCRIPTION

iLocator is an image-based multi-label subcellular location predictor, which covers 7 cellular localizations, i.e. cytoplasm, endoplasmic reticulum, Golgi apparatus, lysosome, mitochondria, nucleus, and vesicles. The iLocator incorporates both global and local image descriptors, and uses an ensemble multi-label classifier to generate accurate predictions.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

iLocator

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 iLocator

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Aug 15;29(16):2032-40. doi: 10.1093/bioinformatics/btt320. Epub 2013 Jun 4.
An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues.
Xu YY1, Yang F, Zhang Y, Shen HB.

AutoChrom3D v1 – Modeling and Visualization the 3D Structure of Human or Mouse Chromatin

AutoChrom3D v1

:: DESCRIPTION

AutoChrom3D was built for modeling and visualization the 3D structure of human or mouse chromatin. The 3D structure of chromatin is calculated and generated based on HiC data.

::DEVELOPER

PENG Cheng (email: pengcheng@mail.hzau.edu.cn).

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl
:: DOWNLOAD

  AutoChrom3D 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Oct;41(19):e183. doi: 10.1093/nar/gkt745. Epub 2013 Aug 21.
The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Peng C1, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT, Zhang HY.