FunSeq2 2.1.6 – Prioritize Regulatory Mutations from Cancer Genome Sequencing

FunSeq2 2.1.6

:: DESCRIPTION

FunSeq2 is specialized to prioritize somatic variants from cancer whole genome sequencing.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FunSeq2

:: MORE INFORMATION

Citation:

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M.
Genome Biol. 2014;15(10):480.

CanBind – Exploring Protein Binding sites Mutated in Cancer

CanBind

:: DESCRIPTION

CanBind is a pipeline to identify genes significantly mutated in cancer

::DEVELOPER

Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

  CanBind

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Feb;42(3):e18. doi: 10.1093/nar/gkt1305. Epub 2013 Dec 19.
Interaction-based discovery of functionally important genes in cancers.
Ghersi D1, Singh M.

Weaver – Allele-Specific Quantification of Structural Variations in Cancer Genomes

Weaver

:: DESCRIPTION

Weaver quantifies allele-specific copy number alteration and allele-specific structural variation in cancer genome using whole-genome sequencing reads.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Weaver

:: MORE INFORMATION

Citation

Allele-Specific Quantification of Structural Variations in Cancer Genomes.
Li Y, Zhou S, Schwartz DC, Ma J.
Cell Syst. 2016 Jul;3(1):21-34. doi: 10.1016/j.cels.2016.05.007.

DawnRank 1.2 – Discovering Personalized Driver Mutations in Cancer

DawnRank 1.2

:: DESCRIPTION

DawnRank is an R package that identifies personalized driver mutations for any given patient sample.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ MacOsX/Linux
  • R

:: DOWNLOAD

DawnRank

:: MORE INFORMATION

Citation:

Genome Med. 2014 Jul 31;6(7):56. doi: 10.1186/s13073-014-0056-8. eCollection 2014.
DawnRank: discovering personalized driver genes in cancer.
Hou JP, Ma J

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.

TCLP – Online Cancer Cell Line Catalogue integrating HLA type

TCLP

:: DESCRIPTION

TCLP (TRON CELL LINE PORTAL)is the largest catalog of cancer cell line annotations integrating HLA type, HLA expression, predicted HLA Class I and Class II neo-epitopes, virus, and gene expression.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Scholtalbers J, Boegel S, Bukur T, Byl M, Goerges S, Sorn P, Loewer M, Sahin U, Castle JC:
TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.
Genome medicine 2015, 7:118.

MUFFINN – Cancer Gene Discovery via Network Analysis of Somatic Mutation data

MUFFINN

:: DESCRIPTION

MUFFINN (MUtations For Functional Impact on Network Neighbors) is a method for prioritizing cancer genes accounting for not only for mutations of individual genes but also those of neighbors in functional networks

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

MUFFINN

:: MORE INFORMATION

Citation

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.
Cho A, Shim JE, Kim E, Supek F, Lehner B, Lee I.
Genome Biol. 2016 Jun 23;17(1):129. doi: 10.1186/s13059-016-0989-x.

BioXpress 3.0 – Gene Expression in Cancer

BioXpress 3.0

:: DESCRIPTION

BioXpress is a gene/miRNA expression and disease association database with expression levels mapped to genes or miRNAs.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.
Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu TJ, Yan C, Zhang H, Mazumder R.
Database (Oxford). 2015 Mar 28;2015. pii: bav019. doi: 10.1093/database/bav019.

BioMuta 4.0 – Single-nucleotide Variations (SNVs) in Cancer

BioMuta 4.0

:: DESCRIPTION

BioMuta is a single-nucleotide variation (SNV) and disease association database where variations are mapped to genomes and RefSeq nucleotide entries, and unified through UniProtKB/Swiss-Prot positional coordinates.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Database (Oxford). 2014 Mar 25;2014:bau022. doi: 10.1093/database/bau022. Print 2014.
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).
Wu TJ1, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R.

xseq 0.2.1 – Assessing Functional Impact on Gene Expression of Mutations in Cancer

xseq 0.2.1

:: DESCRIPTION

Cancer driver mutations control outcomes indirectly through intermediate phenotypes, e.g., gene expression and protein expression. xseq is a probabilistic model which aims to encode the impact of somatic mutations on gene expression profiles.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

xseq

:: MORE INFORMATION

Citation

Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554.
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Ding J et al.