Webtools for microarray data retrieval and analysis allow registered users to download raw data files and annotated microarray chip data files. Chip privileges can also be assigned to other registered users. The gene search utility allows users to query annotations for genes/probesets from Entrez Gene, UniGene, Gene Ontology, and dbSNP and to view expression profile information for genes of interest. Users also have access to microarray raw data files and annotated data for all publications authored by Washington University researchers.
Nagarajan Lab Washington University
Home
Research Publications Projects People Employment/Training Opportunities
 
Chip Import Utility (CIU) is a tool to upload metadata, raw and analyzed data in our database CHIPDB for the microarray experiments (expression and SNP chips) performed by investigators at Washington University
 
Examine gene expression in the context of functional annotations such as biological processes or molecular functions from Gene Ontology, across different microarray experiments of one or more species. Filter genes on the basis of annotations or expression data. Cluster probesets /samples using different supervised / unsupervised clustering techniques.Export /import data to/from another analysis applications
 
LIMS, an application for data management is being developed for the Proteomics core. The application is designed to handle sample curation, processing, image analysis and data reporting.
 
Projects
 
To facilitate clinical and translational research, we are developing caBench-to-Bedside (caB2B). caB2B will be used to query caGrid data services and will analyze this data using caGrid analytical services. In the first year, the scope of caB2B is confined to the query, analysis and visualization of microarray expression data.
caB2B: caB2B is a tool that allows research scientist to obtain the microarray data from caArray and associate it to the biospecimen information from caTissue.
Details Download Use Support 		 
     
caTISSUE Core: A biospecimen inventory informatics system.
Details Demo Download Support
 
caTissue Core is a web-based biospecimen inventory and tracking tool that may be used by biospecimen resource facilities, regardless of the nature of biospecimen transactions that occur or the type of biospecimens involved in the transaction. In the next version of caTissue, it will support integration with associated free-text surgical pathology reports (SPR) and discrete clinical and pathology annotations
 
 
CIU: A tool to upload microarray experiments into our database.
DetailsSupport Use Support 		 
     
 
CRS is developed to facilitate compatibility reviews by the Vocabularies and Common Data Elements (VCDE) and Architecture (ARCH) workspaces. Currently we are developing version 2.0 that will contain tools for compatibility self-checks by developers and reports that determine the true CDE reuse.
CRS: A tool to facilitate caBIGTM Architecture and Vocabularies and Common Data Elements compatibility reviews.
Details Demo Support Use 		 
 
 
Function Express or FE- To analyze microarray expression data, FE allows end users to filter, normalize, cluster, and classify gene expression data. Available algorithms include Significance Analysis of Microarrays (SAM), k-means, hierarchical, and SOM clustering, GenePattern (Consensus Clustering, Comparative Marker Selection, and Weighted Voting), and R modules (SVM and PCA). FE will also allow end users to view gene networks created using co-expression, transcription factor binding site, pathway, interaction, and literature-based data
FE Client:Function Express provides data mining and rich visualization capabilities to view and analyze microarray data in the context of multiple publicly available gene annotation databases. details
Details Demo Download Support 		 
     
 
Examine gene expression in the context of functional annotations such as biological processes or molecular functions from Gene Ontology, across different microarray experiments of one or more species. Filter genes on the basis of annotations or expression data. Cluster probesets /samples using different supervised / unsupervised clustering techniques.Export /import data to/from another analysis applications
FE Server: An automated microarray annotation system.
Details Download Support 		 
 
GeneConnect: A caBIGTM compliant genomic identifier mapping service.
Details Support Use Support 		 
     
LIMS: A management system to track proteomics experiments.
Details Support Use Support 		 
 
 
Mascot Viewer or MaV- To analyze proteomics data, MaV allows users to view a 'clickable' gel and to click on relevant spots to view consolidated (i.e. multiple mass spectrometry [MS] runs on one or more machines) MS and MS/MS results.
Mascot Search: An analytical tool to view protein database search results.
Details Support Use Support 		 
     
Mutation Viewer: A clinical resequencing pipeline.
Details Support Use Support
 
Mutation Viewer or MuV- To analyze re-sequencing data. We are refining the MuV pipeline to allow users to design primers in high throughput using a web interface, to analyze sequence traces for mixed peaks and indels using multiple analytical tools, and to visualize mutation information in the context of genomic annotation (e.g. exon-intron boundaries, protein domains, and known SNPs).
 
 
Promoter Analysis Pipeline: A comprehensive workbench to identify transcription factor binding sites in mammalian genomes.
Details Demo Support Use Support
 
The Promoter Analysis Pipeline (PAP) is a web-based workbench for identifying transcription factor binding sites in a set of coexpressed genes in mammals. PAP is based on a statistical model which predicts the transcriptional factors and their regulatory targets in the genome using overrepresentation of binding profiles in promoter sequences.
 
     
Webtools: Web-based tools to download annotated microarray data, assign chip privileges, and browse gene annotation and expression information.
Details Support Use Support 		 
 
Home
copyright
Support Support