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Links tagged with 'neoplasms'

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Found 16 links

Displaying 15 links

Cancer Genome Anatomy ProjectTool Content

http://cgap.nci.nih.gov/

DNA > Sequence Polymorphisms
Expression > cDNA, EST, SAGE
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Model Organisms > Other Vertebrates

Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.

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tagsgene library human genome project humans neoplasms

CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

NAR Web Server Issue 2007
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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

CaSNPDatabase Content

http://cistrome.dfci.harvard.edu/CaSNP/

Expression > Databases

CaSNP database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization.

NAR Database Issue 2011
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tagsdna copy number variations human genome humans neoplasms nucleic acid databases oligonucleotide array sequence analysis single nucleotide polymorphism

CCancerDatabase Content

http://mips.helmholtz-muenchen.de/proj/ccancer

Expression > Gene Set Analysis
Literature > Open Access Resources

CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.

NAR Web Server Issue 2010
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tagsaniline compounds cell aging data mining genetic databases humans monte carlo method neoplasm genes neoplasm proteins neoplasms neoplastic gene expression regulation nitriles protein kinase inhibitors quinolines

COSMICDatabase Content

http://www.sanger.ac.uk/genetics/CGP/cosmic/

DNA > Databases
Human Genome > Databases

COSMIC curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs. Biomart allows more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus. COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

NAR Database Issue 2010NAR Database Issue 2011
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tagscomputational biology data mining genetic databases human genome humans mutation neoplasms nucleic acid databases protein databases search engine tumor cell line

dbCRIDDatabase Content

http://dbCRID.biolead.org

DNA > Databases

A database of Chromosomal Rearrangements In Diseases (dbCRID, http://dbCRID.biolead.org) is a database of human CR events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the disease or symptoms associated, and--when possible--detailed information about the CR event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover/analyze the CR event.

This content is being maintained by tongbinli.

NAR Database Issue 2011
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tagschromosome aberrations chromosome breakpoints disease factual databases humans neoplasms

dbDEPCDatabase Content

http://lifecenter.sgst.cn/dbdepc/index.do

Human Genome > Databases
Protein > Databases

A database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications.

NAR Database Issue 2010
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tagscomputational biology dna gene expression profiling genetic databases human genome humans neoplasms neoplastic gene expression regulation protein databases proteome rna

GeneHub-GEPISTool Content

http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat

GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.

NAR Web Server Issue 2007
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tagsalgorithms biological tumor markers chromosome mapping dna sequence analysis expressed sequence tags gene expression profiling genetic testing humans neoplasms online systems sequence alignment

GeneSigDBDatabase Content

http://compbio.dfci.harvard.edu/genesigdb

Expression > Databases

GeneSigDB is a manually curated database of gene expression signatures. GeneSigDB focuses on cancer, development, and stem cell gene signatures and was constructed from thousands of publications from which we manually transcribe gene signatures. Gene signatures are mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. GeneSigDB release 3.0 (Decemeber 2010) contained over 2,000 gene signatures.

NAR Database Issue 2010
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tagsalgorithms computational biology gene expression profiling genetic databases humans neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis protein databases stem cells

GlycoViewerTool Content

http://www.systemsbiology.org.au/glycoviewer

Other Molecules > Carbohydrates

The GlycoViewer is a web-based tool that can visualize, summarize and compare sets of gylcan structures.

NAR Web Server Issue 2010
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tagsglycomics glycoproteins humans neoplasms polysaccharides

NCBI Taxonomy DatabaseDatabase Content

http://www.ncbi.nlm.nih.gov/Taxonomy

DNA > Phylogeny Reconstruction
Model Organisms > General Resources
Protein > Phylogeny Reconstruction

Taxonomic classification of all organisms with sequences in GenBank.

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tagsanimals biology dna expressed sequence tags factual databases gene expression genome human genome humans mice molecular models national library of medicine (u.s.) neoplasms phenotype sequence tagged sites united states

Network of Cancer GenesDatabase Content

http://bio.ifom-ieo-campus.it/ncg2

Human Genome > Databases

The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer.

NAR Database Issue 2010
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tagsanimals computational biology gene expression profiling gene regulatory networks genetic databases humans mutation neoplasm genes neoplasms neoplastic gene expression regulation nucleic acid databases plant genome

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2003NAR Web Server Issue 2006NAR Web Server Issue 2007
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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

QuadruplexTool Content

http://www.quadruplex.org

DNA > Structure and Sequence Feature Detection

A website to serve the quadruplex community. Contains conference information, forums, database and parsers.

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tagsanimals antineoplastic agents drug design g-quadruplexes gene expression regulation gene therapy genetic promoter regions guanine humans ligands molecular models molecular structure neoplasms neoplastic gene expression regulation nucleic acid conformation telomere theoretical models

SelTarbaseDatabase Content

http://www.seltarbase.org

Human Genome > Databases

The Selective Targets database is a curated database of a growing number of public mononucleotide repeat tracts (MNR) mutation data in microsatellite unstable human tumors. Regression calculations for various microsatellite instability (MSI) -H tumor entities indicating statistically deviant mutation frequencies predict genes that are shown or highly suspected to be involved in MSI tumorigenesis. Many useful tools for further analyzing genomic DNA, derived wild-type and mutated cDNAs and peptides are integrated. A comprehensive database of all human coding, untranslated, non-coding RNA- and intronic MNRs (MNR_ensembl) is also included.

NAR Database Issue 2010
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tagsamino acid sequence base sequence computational biology dna repair genetic databases humans immune system microsatellite instability microsatellite repeats molecular sequence data mutation neoplasms nucleic acid databases