Tools   Select Another Resource Report Type

http://lab.rockefeller.edu/casanova/HGC

Data set containing a gene-specific connectome file for each human gene and computer programs for ranking lists of genes within a gene-specific connectome, clustering and plotting the genes by the functional genomic alignment (FGA) approach, and generating gene-specific connectomes. The programs were developed and tested on Mac and Linux systems. The external software required for running these programs is open-source and free of charge. The HGC is the set of all biologically plausible routes, distances, and degrees of separation between all pairs of human genes. A gene-specific connectome contains the set of all available human genes sorted on the basis of their predicted biological proximity to the specific gene of interest. The HGC is a powerful approach for human genotype-phenotype high-throughput studies, for which it can be used to rank any list of genes within a gene-specific connectome for an experimentally validated core gene. Functional genomic alignment (FGA) is equivalent to traditional multiple sequence alignment (MSA), except that it clusters genes in trees on the basis of the functional biological distance between them predicted by HGC, rather than on the basis of molecular evolutionary genetic distance. This method is therefore more suitable for disease and phenotypic studies.

Proper citation: Human Gene Connectome (RRID:SCR_002628) Copy   

•   Source: SciCrunch Registry

http://mindboggle.info/data.html

Complete set of free, publicly accessible, downloadable atlases, templates, and individual manually labeled brain image data, the largest collection of publicly available, manually labeled human brains in the world! http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full

Proper citation: Mindboggle-101 atlases (RRID:SCR_002439) Copy   

•   Source: SciCrunch Registry

http://www.genpat.uu.se/mtDB

A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences.

Proper citation: mtDB - Human Mitochondrial Genome Database (RRID:SCR_002945) Copy   

•   Source: SciCrunch Registry

http://edas2.bioinf.fbb.msu.ru/

Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test.

Proper citation: EDAS - EST-Derived Alternative Splicing Database (RRID:SCR_002449) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases

3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old.

Proper citation: UNC Infant 0-1-2 Atlases (RRID:SCR_002569) Copy   

•   Source: SciCrunch Registry

http://www.mitomap.org/

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

Proper citation: MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) Copy   

•   Source: SciCrunch Registry

http://hgc.rockefeller.edu/

An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.

Proper citation: Human Gene Connectome Server (RRID:SCR_002627) Copy   

•   Source: SciCrunch Registry

http://www.depressiontools.org/

Online instrument that estimates whether a biomarker predicting outcome of depression treatment is likely to be clinically significant.

Proper citation: DepressionTools.org Clinical Significance Calculator (RRID:SCR_003873) Copy   

•   Source: SciCrunch Registry

http://www.umassmed.edu/iscr/

A registry of stem cell lines that provides a searchable database that includes published and validated unpublished information on human embryonic (hESC) and disease-specific induced pluripotent (iPS) stem cell lines. The Registry will include information on cell lines from non-profit institutions, academic centers, stem cell banks and industry based in the United States and abroad. The International Stem Cell Registry is developed in partnership with and funded by the Massachusetts Life Sciences Center. The work of the registry is made possible by the MLSC and important collaborators, including the Harvard Stem Cell Institute.

Proper citation: International Stem Cell Registry (RRID:SCR_003653) Copy   

•   Source: SciCrunch Registry

http://people.biochem.umass.edu/fournierlab/3dmodmap/

Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.

Proper citation: 3D Ribosomal Modification Maps Database (RRID:SCR_003097) Copy   

•   Source: SciCrunch Registry

http://mutdb.org/

Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene.

Proper citation: MutDB (RRID:SCR_003251) Copy   

•   Source: SciCrunch Registry

http://genomequebec.mcgill.ca/PReMod

Database that describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide / transcription factor-wide collection of predicted regulatory modules for the human genome. The algorithm used involves two steps: (i) Identification and scoring of putative transcription factor binding sites using 481 TRANSFAC 7.2 position weight matrices (PWMs) for vertebrate transcription factors. To this end, each non-coding position of the human genome was evaluated for its similarity to each PWM using a log-likelihood ratio score with a local GC-parameterized third-order Markov background model. Corresponding orthologous positions in mouse and rat genomes were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned positions (based on a Multiz (Blanchette et al. 2004) genome-wide alignment of these three species) was used to define the matrix score for each genomic position and each PWM. (ii) Detection of clustered putative binding sites. To assign a module score to a given region, the five transcription factors with the highest total scoring hits are identified, and a p-value is assigned to the total score observed of the top 1, 2, 3, 4, or 5 factors. The p-value computation takes into consideration the number of factors involved (1 to 5), their total binding site scores, and the length and GC content of the region under evaluation. Users can retrieve all information for a given region, a given PWM, a given gene and so on. Several options are given for textual output or visualization of the data.

Proper citation: PReMod (RRID:SCR_003403) Copy   

•   Source: SciCrunch Registry

http://aging.ucsd.edu/news.php

A list of articles published related to aging produced by the Center for Healthy Aging, Stein Institute for Research on Aging.

Proper citation: Stein Institute for Research on Aging News (RRID:SCR_003760) Copy   

•   Source: SciCrunch Registry

http://mirnamap.mbc.nctu.edu.tw

A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA.

Proper citation: miRNAMap (RRID:SCR_003156) Copy   

•   Source: SciCrunch Registry

http://ixdb.mpimg-berlin-dahlem.mpg.de

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A repository for physical mapping data of the human X chromosome that aims at providing a global view of genomic data at a chromosomal level including an integrated physical, genetic, transcript and sequence map of the human X chromosome. This implies acquiring, understanding and formatting an enormous amount of experimental results and can only be accomplished progressively. We have chosen to start the integration process with YAC maps generated by the community. These provide the basis for future higher resolution physical maps, as well as emerging transcript and sequence maps. The current content of IXDB therefore reflects this situation, with the emphasis placed on YAC mapping data. Due to their immediate value, IXDB has also started to systematically include bacterial clone contig maps and EST data. Currently IXDB does not store sequence data, although links to nucleic sequence databases are provided.

Proper citation: Integrated X Chromosome Database (RRID:SCR_003028) Copy   

•   Source: SciCrunch Registry

http://compbio.uthsc.edu/miRSNP/

Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.

Proper citation: PolymiRTS (RRID:SCR_003389) Copy   

•   Source: SciCrunch Registry

http://ratmap.gen.gu.se/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process.

Proper citation: Rat Gene Symbol Tracker (RRID:SCR_003261) Copy   

•   Source: SciCrunch Registry

http://www.nephromine.org/

THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data.

Proper citation: Nephromine (RRID:SCR_003813) Copy   

•   Source: SciCrunch Registry

http://bioinfo.mbi.ucla.edu/ASAP/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases.

Proper citation: ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) Copy   

•   Source: SciCrunch Registry

http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

•   Source: SciCrunch Registry