> > Transcript Expression Analysis

Transcript Expression Analysis

This section contains links to microarray methods, standards for microarray data, and analysis tools for expression data from other high-throughput technologies. Also contains tools for transcript expression in general.

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Found 105 links

Displaying 15 links

ACIDDatabase Content

http://bioinfo.thep.lu.se/acid.html

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.

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tagsanimals chromosome mapping database management systems genetic databases human genome humans mice molecular cloning oligonucleotide array sequence analysis

ACTTool Content

http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php

Expression > Transcript Expression Analysis
Model Organisms > Plants

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

NAR Web Server Issue 2006
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tagsalgorithms arabidopsis circadian rhythm gene expression profiling oligonucleotide array sequence analysis plant genes transcription factors

Affymetrix NetAffx Analysis CenterDatabase Content

http://www.affymetrix.com/analysis/index.affx

Expression > Transcript Expression Analysis

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

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tagsanimals consensus sequence gene expression profiling genetic databases markov chains oligonucleotide array sequence analysis protein sequence analysis proteins

AMIC@Tool Content

http://bioalgo.iit.cnr.it/amica

Expression > Transcript Expression Analysis

The All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.

NAR Web Server Issue 2008
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tagsalgorithms cluster analysis gene expression profiling oligonucleotide array sequence analysis

ArrayExpressDatabase Content

http://www.ebi.ac.uk/arrayexpress/

Expression > Transcript Expression Analysis

Public repository for microarray based gene expression data; contains several curated gene expression datasets.

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tagsalgorithms animals computational biology data collection database management systems europe gene expression profiling genetic databases information dissemination information systems oligonucleotide array sequence analysis proteins software design

ArrayPipeTool Content

http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl

Expression > Transcript Expression Analysis

ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.

NAR Web Server Issue 2004
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tagsgene expression profiling oligonucleotide array sequence analysis

ArrayXPathTool Content

http://www.snubi.org/software/ArrayXPath/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.

NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagscluster analysis gene expression profiling genetic databases genetic predisposition to disease medical subject headings oligonucleotide array sequence analysis signal transduction statistical data interpretation systems integration

AsteriasTool Content

http://asterias.bioinfo.cnio.es/

DNA > Annotations
Expression > Transcript Expression Analysis

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.

This content is being maintained by rdiaz02.

NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition automation cluster analysis computational biology computer simulation database management systems dna sequence analysis gene expression profiling genetic models genomics humans nucleic acid hybridization oligonucleotide array sequence analysis programming languages sequence alignment statistical models

AutoClass@IJMTool Content

http://www.ijm.fr/en/ijm/resources/bioinformatics/

Expression > Gene Set Analysis
Expression > Protein Expression
Expression > Transcript Expression Analysis
Human Genome > Genomics
Protein > Protein Expression

AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.

NAR Web Server Issue 2009
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tagsalgorithms bayes theorem classification cluster analysis gene expression profiling oligonucleotide array sequence analysis

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

NAR Web Server Issue 2004
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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

BioconductorTool Content

http://www.bioconductor.org/

Computer Related > Bio-* Programming Tools
Computer Related > Math and Statistics
Expression > Transcript Expression Analysis

Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.

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tagsalgorithms biological models computational biology computer simulation database management systems dna probes dna sequence analysis gene expression profiling gene expression regulation information dissemination nucleic acid sequence homology oligonucleotide array sequence analysis reproducibility of results sequence alignment signal transduction transcription factors

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, 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.

NAR Web Server Issue 2006
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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

Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Interactions, Pathways, 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.

NAR Web Server Issue 2010
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tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

NAR Web Server Issue 2008
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tagsalgorithms cluster analysis computational biology gene expression profiling

Tags associated with subcategory 'Expression/Transcript Expression Analysis'

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