cDNA, EST, SAGE

Links to clone repositories, expression data, methods, and tools for expressed sequence tags (EST) and serial analysis of gene expression (SAGE) are found here.

Found 43 links

Displaying 15 links

ACIDDatabase Content

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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.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
ACID: a database for microarray clone information200418

ALGGENTool Content

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ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

Allen Brain AtlasDatabase Content

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The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region.

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ASPicTool Content

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Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

BabelomicsTool Content

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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.

Cancer Genome Anatomy ProjectTool Content

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Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.

DEEPTool Content

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DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
DEEP--a tool for differential expression effector prediction20072

diArk - a resource for eukaryotic genome researchDatabase Content

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diArk is a database driven web application that is designed to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes.

DiscoverySpaceTool Content

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DiscoverySpace is a tool for gene expression analyses and biological discovery.

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E2GTool Content

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E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.

EGassemblerTool Content

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EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.

This content is being maintained by amasoudin.

ENDEAVOURTool Content

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ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

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