> Tag > Links tagged with 'gene expression profiling'

Links tagged with 'gene expression profiling'

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV

Found 143 links

Displaying 15 links

Hide Resources (3)Hide Databases (47)Hide Tools (93)

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/ [open in a new window]

Share This Link
DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

This content is being maintained by kimmen.

links directory index: 4963
TitlePublication YearGoogle Scholar Citation Count
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis200720
MUSCLE: multiple sequence alignment with high accuracy and high throughput20044855
SATCHMO: sequence alignment and tree construction using hidden Markov models200388
Phylogenetic inference in protein superfamilies: analysis of SH2 domains.19980
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/ [open in a new window]

Share This Link
Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
BiologicalNetworks: visualization and analysis tool for systems biology200664
PathSys: integrating molecular interaction graphs for systems biology.20060
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbiological models computer simulation gene expression profiling genetic databases genomics oligonucleotide array sequence analysis protein databases protein interaction mapping saccharomyces cerevisiae proteins signal transduction systems biology systems integration

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet [open in a new window]

Share This Link
Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
BioMet Toolbox: genome-wide analysis of metabolism201017
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/ [open in a new window]

Share This Link
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

links directory index: 702
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes2001670
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

BioverseTool Content

http://bioverse.compbio.washington.edu/ [open in a new window]

Share This Link
DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
Functional annotation from predicted protein interaction networks200537
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes200513
Enhanced functional information from predicted protein networks200420
Bioverse: Functional, structural and contextual annotation of proteins and proteomes200325
NAR Web Server Issue 2005NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

BTWTool Content

http://bioinformatics.bc.edu/clotelab/BTW/ [open in a new window]

Share This Link
Expression > Transcript Expression Analysis

Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann\' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
BTW: a web server for Boltzmann time warping of gene expression time series20062
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms gene expression profiling genomics humans sequence alignment time factors

CARMAwebTool Content

https://carmaweb.genome.tugraz.at/carma/ [open in a new window]

Share This Link
Expression > Transcript Expression Analysis

Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.

This content is being maintained by johannes.rainer.

links directory index: 103
TitlePublication YearGoogle Scholar Citation Count
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis2006103
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscluster analysis controlled vocabulary gene expression profiling oligonucleotide array sequence analysis

CARRIETool Content

http://zlab.bu.edu/CARRIE-web [open in a new window]

Share This Link
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis200430
Questions and answers about AIDS.19920
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsacquired immunodeficiency syndrome binding sites computational biology dna female gene expression profiling gene expression regulation genetic promoter regions genetic transcription hiv hiv infections humans male newborn infant nucleic acid regulatory sequences nurses oligonucleotide array sequence analysis physicians pregnancy transcription factors

ChimerDBDatabase Content

http://ercsb.ewha.ac.kr/fusiongene [open in a new window]

Share This Link
DNA > Databases

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChimerDB 2.0--a knowledgebase for fusion genes updated20106
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsalgorithms animals chromosomes computational biology expressed sequence tags gene expression profiling gene fusion genetic databases genetic translocation genomics humans information storage and retrieval internet messenger rna mice mutant chimeric proteins nucleic acid databases protein databases pubmed rats software user-computer interface

ChIP-ArrayTool Content

http://wanglab.hku.hk/ChIP-Array [open in a new window]

Share This Link
Expression > Gene Regulation

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor20113
NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals binding sites chromatin immunoprecipitation gene expression profiling high-throughput nucleotide sequencing humans mice oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

ChipInfoTool Content

http://genomics.bioen.illinois.edu/chipinfo/ [open in a new window]

Share This Link
Expression > Transcript Expression Analysis

ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis200395
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsdna probes gene expression profiling genetic databases oligonucleotide array sequence analysis systems integration

CIBEXDatabase Content

http://cibex.nig.ac.jp/ [open in a new window]

Share This Link
Expression > Transcript Expression Analysis

The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

links directory index: 226
TitlePublication YearGoogle Scholar Citation Count
Submission of microarray data to public repositories200494
CIBEX: center for information biology gene expression database2003132
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscomputational biology database management systems forecasting gene expression gene expression profiling genetic databases information systems oligonucleotide array sequence analysis software design

CIPRO 2.5Database Content

http://cipro.ibio.jp/2.5 [open in a new window]

Share This Link
Model Organisms > Databases

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The CIPRO database collects published data as well as unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data. Homologs in humans and major model organisms are included. Annotations are open to evaluation by users through the CIPRO website.

This content is being maintained by tendo.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality20116
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence animals ciona intestinalis computational biology gene expression profiling genomics molecular sequence annotation protein databases proteome proteomics systems integration

CMATool Content

http://www.gene-regulation.com/pub/programs/cma/CMA.html [open in a new window]

Share This Link
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

links directory index: 66
TitlePublication YearGoogle Scholar Citation Count
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm200623
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations200643
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acid sequence binding sites chemical models computer simulation dna sequence analysis endothelial cells gene expression profiling genetic promoter regions humans molecular sequence data protein binding protein sequence analysis transcription factors

CoPubTool Content

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

Share This Link
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics

CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
CoPub: a literature-based keyword enrichment tool for microarray data analysis200833
NAR Web Server Issue 2008NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals gene expression profiling humans medline mice oligonucleotide array sequence analysis rats

Associated Tag Cloud