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Links tagged with 'phenotype'

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Found 33 links

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AspGDDatabase Content

http://www.aspergillusgenome.org/ [open in a new window]

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Model Organisms > Databases

The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community201021
NAR Database Issue 2010
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tagsaspergillus nidulans computational biology fungal genes fungal genome fungal proteins genetic databases genetic models genetics nucleic acid databases phenotype protein databases tertiary protein structure

Defining Transcriptional Programs in Vascular EndotheliumResource Content

http://www.vessels.bwh.harvard.edu/ [open in a new window]

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Expression > Gene Regulation
Expression > Transcript Expression Analysis

This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.

links directory index: 398
TitlePublication YearGoogle Scholar Citation Count
Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation200426
Biomechanical activation of vascular endothelium as a determinant of its functional phenotype2001355
Argus--a new database system for Web-based analysis of multiple microarray data sets200117
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tagsbase sequence biomechanics complementary dna cultured cells dna primers factual databases gene expression profiling humans molecular sequence data nucleic acid hybridization oligonucleotide array sequence analysis phenotype reproducibility of results statistics as topic vascular endothelium

E-RNAiTool Content

http://e-rnai.dkfz.de/ [open in a new window]

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DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

links directory index: 579
TitlePublication YearGoogle Scholar Citation Count
E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update20104
E-RNAi: a web application to design optimized RNAi constructs200565
Genome-wide RNAi analysis of growth and viability in Drosophila cells2004510
NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

EuroPhenomeDatabase Content

http://www.europhenome.org/ [open in a new window]

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Model Organisms > Databases

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or the predicted phenotype.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
EuroPhenome: a repository for high-throughput mouse phenotyping data201022
NAR Database Issue 2010
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tagsanimals computational biology genetic databases inbred c57bl mice inbred strains mice knockout mice mice phenotype programming languages protein databases tertiary protein structure

FastSNPTool Content

http://fastsnp.ibms.sinica.edu.tw [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Function Analysis and Selection Tool for Single Nucleotide Polymorphisms (FastSNP) allows users to identify and prioritize SNPs that are likely to have functional effects.

This content is being maintained by fastsnp.

links directory index: 228
TitlePublication YearGoogle Scholar Citation Count
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization2006228
NAR Web Server Issue 2006
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tagsgene frequency genetic predisposition to disease phenotype proteins risk single nucleotide polymorphism

Filamentous Fungal Gene Expression Database (FFGED)Database Content

http://bioinfo.townsend.yale.edu/ [open in a new window]

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Expression > Databases
Model Organisms > Databases

The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.

This content is being maintained by Jeffrey P. Townsend.

links directory index: 158
TitlePublication YearGoogle Scholar Citation Count
Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons200741
Enabling a community to dissect an organism: overview of the Neurospora functional genomics project200764
Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination200553
NAR Web Server Issue 2005
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tagsalgorithms amitrole animals base sequence basic-leucine zipper transcription factors bayes theorem ChIP-seq chromosome mapping cluster analysis computational biology computer graphics database management systems dictyostelium dna-binding proteins enzyme inhibitors experimental design expressed sequence tags fungal dna fungal gene expression regulation fungal genes fungal genome fungal proteins fungal spores gene deletion gene expression gene expression profiling gene library genetic databases genetic models genetic promoter regions genetic techniques genetic transcription genomics internet messenger rna microarray molecular sequence data mutation neurospora neurospora crassa northern blotting nucleic acid databases oligonucleotide array sequence analysis oligonucleotide probes phenotype regulon related experiments reproducibility of results rna-seq saccharomyces cerevisiae saccharomyces cerevisiae proteins sequence alignment single nucleotide polymorphism software statistical models systems integration transcription factors user-computer interface ustilago

G2DTool Content

http://www.ogic.ca/projects/g2d_2/ [open in a new window]

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Human Genome > Health and Disease

G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.

links directory index: 486
TitlePublication YearGoogle Scholar Citation Count
Update of the G2D tool for prioritization of gene candidates to inherited diseases200737
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes200685
G2D: a tool for mining genes associated with disease2005112
Association of genes to genetically inherited diseases using data mining2002252
NAR Web Server Issue 2007
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tagsalgorithms alzheimer disease asthma chromosome mapping computational biology genes genetic databases genetic linkage genetic markers genetic predisposition to disease human genome humans inborn genetic diseases mathematics medline obesity phenotype type 2 diabetes mellitus

genenames.orgDatabase Content

http://www.genenames.org [open in a new window]

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Literature > Databases

genenames.org displays all approved nomenclature within Symbol Reports that contain data curated by HUGO Gene Nomenclature Committee (HGNC) editors and links to related genomic, phenotypic and proteomic information. New features include a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility.

This content is being maintained by HGNC.

links directory index: 296
TitlePublication YearGoogle Scholar Citation Count
genenames.org: the HGNC resources in 2011201136
The HGNC Database in 2008: a resource for the human genome2008125
Genew: the Human Gene Nomenclature Database, 2004 updates2004135
NAR Database Issue 2011
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external linksLink on Twitter Link on Wikipedia
tagsanimals computational biology gene symbols genes genetic databases genetic variation genomics human genome humans information storage and retrieval internet mice nomenclature phenotype proteomics software systems integration terminology as topic user-computer interface

GeneSeekerTool Content

http://www.cmbi.ru.nl/GeneSeeker/ [open in a new window]

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Human Genome > Health and Disease

GeneSeeker allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases.

links directory index: 67
TitlePublication YearGoogle Scholar Citation Count
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases200567
NAR Web Server Issue 2005
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tagschromosome mapping gene expression genetic databases genetic predisposition to disease humans inborn genetic diseases phenotype syndrome systems integration

Geno2phenoTool Content

http://www.geno2pheno.org/cgi-bin/geno2pheno.pl [open in a new window]

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Model Organisms > Other Organisms

Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.

links directory index: 363
TitlePublication YearGoogle Scholar Citation Count
Methods for optimizing antiviral combination therapies200342
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes2003147
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype2002174
NAR Web Server Issue 2003
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tagsalgorithms anti-hiv agents artificial intelligence automated pattern recognition cluster analysis computational biology computer-assisted drug therapy computing methodologies decision trees disease susceptibility dna sequence analysis drug combinations factual databases gene expression profiling genetic models genetic polymorphism genetic variation genotype hiv hiv infections hiv-1 humans innate immunity molecular sequence data phenotype pol genes regression analysis reproducibility of results sensitivity and specificity statistical models viral dna viral drug resistance viral genome

GFINDerTool Content

http://www.medinfopoli.polimi.it/GFINDer/ [open in a new window]

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Expression > Transcript Expression Analysis

Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.

links directory index: 115
TitlePublication YearGoogle Scholar Citation Count
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists200552
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining200463
NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagscomputational biology controlled vocabulary gene expression profiling genetic databases genomics humans inborn genetic diseases oligonucleotide array sequence analysis phenotype proteins statistical data interpretation systems integration

IKMCDatabase Content

http://www.knockoutmouse.org [open in a new window]

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Model Organisms > Databases

The International Knockout Mouse Consortium (IKMC) database and web portal serves as the central public web site for IKMC data. Researchers can access up-to-date information on IKMC knockout vectors, ES cells and mice for specific genes, and follow links to the respective repositories from which corresponding IKMC products can be ordered. Researchers can also use the web site to nominate genes for targeting, or to indicate that targeting of a gene should receive high priority. The IKMC database provides data to, and features extensive interconnections with, other community databases.

This content is being maintained by damiansmedley.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
BioMart as an integration solution for the International Knockout Mouse Consortium20112
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium201114
NAR Database Issue 2011
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tagsalleles animals biomedical research database management systems embryonic stem cells gene knockout techniques gene targeting genetic databases genetic vectors genomics humans international cooperation knockout mice mice molecular sequence annotation phenotype societies

ISTECH SNPAnalyzerTool Content

http://snp.istech.info/istech/board/login_form.jsp [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

ISTECH SNPAnalyzer is a tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required; some browser requirements and set-up necessary.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis200538
NAR Web Server Issue 2005
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tagsalgorithms dna sequence analysis gene frequency genetic predisposition to disease genotype haplotypes humans linkage disequilibrium phenotype quantitative trait loci single nucleotide polymorphism systems integration

MIPSDatabase Content

http://www.helmholtz-muenchen.de/en/ibis [open in a new window]

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Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

links directory index: 703
TitlePublication YearGoogle Scholar Citation Count
MIPS: curated databases and comprehensive secondary data resources in 201020119
MIPS: analysis and annotation of proteins from whole genomes2004422
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics200487
MOsDB: an integrated information resource for rice genomics200317
Sputnik: a database platform for comparative plant genomics200350
The PEDANT genome database2003118
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tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology data mining dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans information storage and retrieval internet metabolomics mice micrornas neoplasm genes nucleic acid databases nucleic acid sequence homology oryza sativa phenotype plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology software systems integration user-computer interface

MIPSDatabase Content

http://mips.helmholtz-muenchen.de [open in a new window]

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Protein > Databases

The Munich Information Center for Protein Sequences (MIPS) provides annotated collections of biological data. High-quality reference resources include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
MIPS: curated databases and comprehensive secondary data resources in 201020119
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsdata mining genetic databases genomics metabolomics micrornas neoplasm genes phenotype plant genome protein databases protein sequence analysis proteomics systems integration

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