Tag: Cancer

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.

ApoCanD – Database of Human Apoptotic Proteins in the Context of Cancer

ApoCanD

:: DESCRIPTION

ApoCanD is a database comprises of crucial information of apoptosis proteins in the context of cancer.This database will facilitate the research community working in the field of apoptosis and cancer.

::DEVELOPER

ApoCanD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ApoCanD: Database of human apoptotic proteins in the context of cancer.
Kumar R, Raghava GP.
Sci Rep. 2016 Feb 10;6:20797. doi: 10.1038/srep20797.

CancerDR – Cancer Drug Resistance Database

CancerDR

:: DESCRIPTION

CancerDR is a database of 148 anticancer drugs and their effectiveness against around 1000 cancer cell lines.

::DEVELOPER

CancerDR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Managing Drug Resistance in Cancer: Role of Cancer Informatics.
Gautam A, Chaudhary K, Kumar R, Gupta S, Singh H, Raghava GP.
Methods Mol Biol. 2016;1395:299-312. doi: 10.1007/978-1-4939-3347-1_17.

Cancertope – Designing genome-based Personalized Immunotherapy or Vaccine against Cancer

Cancertope

:: DESCRIPTION

Cancertope is a platform which developed for designing genome-based immunotherapy or vaccine against a cancer cell.

::DEVELOPER

Cancertope team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
Gupta S, Chaudhary K, Dhanda SK, Kumar R, Kumar S, Sehgal M, Nagpal G, Raghava GP.
PLoS One. 2016 Nov 10;11(11):e0166372. doi: 10.1371/journal.pone.0166372.

CancerPDF – Cancer Peptidome Database of BioFluids

CancerPDF

:: DESCRIPTION

CancerPDF is a manually curated database of cancer-associated peptides found in different human bodyfluids (e.g., serum, urine, plasma and saliva). These peptides were experimentally identified using diffrent techniques of proteomics. It covers nearly 30 types of human cancers.

::DEVELOPER

CancerPDF team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CancerPDF: A repository of cancer-associated peptidome found in human biofluids.
Bhalla S, Verma R, Kaur H, Kumar R, Usmani SS, Sharma S, Raghava GPS.
Sci Rep. 2017 May 4;7(1):1511. doi: 10.1038/s41598-017-01633-3.

CancerPred – Prediction of Cancer Lectins

CancerPred

:: DESCRIPTION

CancerPred is a web-server specially trained for predicting the Cancerlectins. Lectins are important biomolecules and play important functions in many processes e.g cell to cell recognition, host-pathogen interactions etc. In the same way Cancerlectins are those lectins which are known to play roles in cancer metastasis and tumor progress, oncogenesis etc. CancerPred is mainly designed for distinguishing Cancerlectins from Non-cancer lectins.

::DEVELOPER

CancerPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Res Notes. 2011 Jul 20;4:237. doi: 10.1186/1756-0500-4-237.
Analysis and prediction of cancerlectins using evolutionary and domain information.
Kumar R1, Panwar B, Chauhan JS, Raghava GP.

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