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http://xin.cz3.nus.edu.sg/group/trmp/trmp.asp

The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore.

Proper citation: Therapeutically Relevant Multiple Pathways Database (RRID:SCR_013471) Copy   

•   Source: SciCrunch Registry

http://signal.salk.edu/cgi-bin/RiceGE

Gene database for Japonica rice. RiceGE is associated with SIGnAL at the Salk Institute.

Proper citation: RiceGE (RRID:SCR_015061) Copy   

•   Source: SciCrunch Registry

http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

https://ckb.jax.org/

Semi-automated and manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and oncology clinical trials. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials.

Proper citation: Jackson Laboratory Clinical Knowledgebase (RRID:SCR_014965) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/humanDisease.shtml

Collection of published and potential mouse models of human disease, discovery of candidate genes and investigation of phenotypic similarity between mouse models and human patients. Mouse mutation, and phenotype and disease model data from Mouse Genome Informatics database are integrated with human gene to disease relationships from the National Center for Biotechnology Information and Online Mendelian Inheritance in Man and human disease to phenotype relationships from the Human Phenotype Ontology.

Proper citation: Human Mouse Disease Connection (RRID:SCR_017522) Copy   

•   Source: SciCrunch Registry

http://www.gcbi.com.cn

Database provides information on research status of gene related diseases, gene expression in different tissues, regulatory relationship among genes, information of diseases, mRNA, Transcription Fctor, miRNA and other information shared among genes.

Proper citation: GCBI database (RRID:SCR_018971) Copy   

•   Source: SciCrunch Registry

http://catlas.org/mousebrain/#!/

Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans.

Proper citation: CATlas (RRID:SCR_018690) Copy   

•   Source: SciCrunch Registry

https://www.sdu.dk/da/Om_SDU/Institutter_centre/Ist_sundhedstjenesteforsk/Centre/DTR.aspx?sideid=index&sprog=eng

Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years.

Proper citation: Danish Twin Registry (RRID:SCR_017482) Copy   

•   Source: SciCrunch Registry

http://epifactors.autosome.ru/

Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.

Proper citation: EpiFactors (RRID:SCR_016956) Copy   

•   Source: SciCrunch Registry

https://hive.biochemistry.gwu.edu/dna.cgi?cmd=tissue_codon_usage&id=586358&mode=cocoputs

Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data.

Proper citation: Codon and Codon-Pair Usage Tables (RRID:SCR_018504) Copy   

•   Source: SciCrunch Registry

http://cometa.tigem.it/

Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions.

Proper citation: CoMeTa Website (RRID:SCR_017357) Copy   

•   Source: SciCrunch Registry

http://mouse.brain-map.org/

Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain.

Proper citation: ABA Mouse Brain: Atlas (RRID:SCR_017479) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/pubs/MitoCarta/

Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.

Proper citation: MitoCarta (RRID:SCR_018165) Copy   

•   Source: SciCrunch Registry

http://diabetes.wisc.edu/index.php

Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.

Proper citation: Attie Lab Diabetes Database (RRID:SCR_016639) Copy   

•   Source: SciCrunch Registry

http://mousebrain.org/

Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.

Proper citation: mousebrain.org (RRID:SCR_016999) Copy   

•   Source: SciCrunch Registry

https://resistomedb.com

Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class.

Proper citation: ResistomeDB (RRID:SCR_018305) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/gsea/msigdb/index.jsp

Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.

Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy   

•   Source: SciCrunch Registry

http://david.abcc.ncifcrf.gov/content.jsp?file=/ease/ease1.htm&type=1

Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible

Proper citation: EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/SCENIC

Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data.

Proper citation: SCENIC (RRID:SCR_017247) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4363993

Software tool by Applied Biosystems to design primers and probes using TaqMan and SYBR Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed for use with StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems. Provides customized application specific documents for absolute⁄relative quantitation and allelic discrimination.

Proper citation: Primer Express Software (RRID:SCR_017376) Copy   

•   Source: SciCrunch Registry