> Tag > Links tagged with 'statistical data interpretation'

Links tagged with 'statistical data interpretation'

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Found 23 links

Displaying 15 links

Resources (0) Databases (0) Tools (23)

DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp [open in a new window]

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DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

links directory index: 3468
TitlePublication YearGoogle Scholar Citation Count
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists2007161
DAVID: Database for Annotation, Visualization, and Integrated Discovery20033307
NAR Web Server Issue 2007
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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

NDB ToolsTool Content

http://ndbserver.rutgers.edu/services/ [open in a new window]

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RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.

links directory index: 1276
TitlePublication YearGoogle Scholar Citation Count
Tools for the automatic identification and classification of RNA base pairs2003125
Geometric nomenclature and classification of RNA base pairs2001373
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids1992778
NAR Web Server Issue 2003
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tagsalgorithms base pairing base sequence chemical models dna factual databases molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology proteins restriction mapping ribosomal rna rna signal recognition particle statistical data interpretation stereoisomerism terminology as topic water

PolyBayesTool Content

http://bioinformatics.bc.edu/marthlab/PolyBayes [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

UNIX-based SNP discovery from redundant sequences; integrated with Phred/Phrap/Consed infrastructure (see DNA -- Contig Assembly); free for non-commercial use.

links directory index: 395
TitlePublication YearGoogle Scholar Citation Count
A general approach to single-nucleotide polymorphism discovery1999395
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tagsalgorithms alleles bayes theorem expressed sequence tags genetic techniques genetic variation human genome humans sequence alignment single nucleotide polymorphism statistical data interpretation

ASIANTool Content

http://eureka.cbrc.jp/asian/ [open in a new window]

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Expression > Transcript Expression Analysis

ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.

links directory index: 287
TitlePublication YearGoogle Scholar Citation Count
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles200523
ASIAN: a website for network inference200417
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling2002186
Statistical estimation of cluster boundaries in gene expression profile data200161
NAR Web Server Issue 2005
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tagsanalysis of variance bayes theorem biological models cluster analysis computational biology computer simulation factual databases fungal genes gene expression gene expression profiling gene expression regulation genetic models oligonucleotide array sequence analysis proteome regression analysis saccharomyces cerevisiae signal transduction statistical data interpretation statistical models

KOBASTool Content

http://kobas.cbi.pku.edu.cn [open in a new window]

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DNA > Annotations
Human Genome > Databases
Protein > Networks & Interactions, Pathways and Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

links directory index: 215
TitlePublication YearGoogle Scholar Citation Count
KOBAS server: a web-based platform for automated annotation and pathway identification200675
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary2005140
NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

YMF 3.0Tool Content

http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.pl [open in a new window]

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DNA > Structure and Sequence Feature Detection

YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.

links directory index: 181
TitlePublication YearGoogle Scholar Citation Count
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation2003181
NAR Web Server Issue 2003
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tagsalgorithms binding sites dna sequence analysis genetic promoter regions mycobacterium tuberculosis nucleic acid regulatory sequences saccharomyces cerevisiae statistical data interpretation transcription factors

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/ [open in a new window]

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DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

links directory index: 120
TitlePublication YearGoogle Scholar Citation Count
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments2007120
NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

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

ArrayXPathTool Content

http://www.snubi.org/software/ArrayXPath/ [open in a new window]

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Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and 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.

links directory index: 111
TitlePublication YearGoogle Scholar Citation Count
ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics200543
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics200468
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

VAMPIRETool Content

http://genome.ucsd.edu/microarray/ [open in a new window]

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Expression > Transcript Expression Analysis

VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.

links directory index: 111
TitlePublication YearGoogle Scholar Citation Count
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data200554
Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes200457
NAR Web Server Issue 2005
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tags3t3-l1 cells adipocytes algorithms animals bayes theorem biological models database management systems dimethyl sulfoxide gene expression profiling gene expression regulation genetic variation mice oligonucleotide array sequence analysis statistical data interpretation statistical models thiazolidinediones transcription factors

POXOTool Content

http://www.bioinfo.biocenter.helsinki.fi/poxo [open in a new window]

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

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.

This content is being maintained by mkankain.

links directory index: 92
TitlePublication YearGoogle Scholar Citation Count
POXO: a web-enabled tool series to discover transcription factor binding sites20067
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets200510
Theme discovery from gene lists for identification and viewing of multiple functional groups200545
POBO, transcription factor binding site verification with bootstrapping200430
NAR Web Server Issue 2006
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tagsarabidopsis binding sites cluster analysis computational biology dna sequence analysis down-regulation gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics hydrogen peroxide itraconazole oligonucleotide array sequence analysis reproducibility of results software design statistical data interpretation transcription factors transcriptional regulatory elements up-regulation

QUMATool Content

http://quma.cdb.riken.jp/ [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. Users can also control the quality of aligned sequences by changing cutoff paramteres.

links directory index: 61
TitlePublication YearGoogle Scholar Citation Count
QUMA: quantification tool for methylation analysis200861
NAR Web Server Issue 2008
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tagscpg islands dna methylation dna sequence analysis statistical data interpretation sulfites

NQ-FlipperTool Content

https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php [open in a new window]

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Protein > 3-D Structure Prediction

NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.

links directory index: 55
TitlePublication YearGoogle Scholar Citation Count
NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures200718
Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures200618
NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures200619
NAR Web Server Issue 2007
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tagsamides asparagine computational biology crystallography escherichia coli glutamine molecular conformation molecular models protein conformation protein databases protein folding proteins reproducibility of results statistical data interpretation stereoisomerism structural models thermodynamics

MIDAWTool Content

http://midaw.cribi.unipd.it/dnachip/ [open in a new window]

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Expression > Transcript Expression Analysis

MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
MIDAW: a web tool for statistical analysis of microarray data200538
NAR Web Server Issue 2005
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tagsalgorithms gene expression profiling normal distribution oligonucleotide array sequence analysis statistical data interpretation

JProGOTool Content

http://www.jprogo.de/index.jsp [open in a new window]

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Expression > Transcript Expression Analysis
Model Organisms > Microbes

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information200626
NAR Web Server Issue 2006
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tagsarchaea archaeal genes bacteria bacterial genes controlled vocabulary gene expression profiling oligonucleotide array sequence analysis statistical data interpretation

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