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http://amp.pharm.mssm.edu/LJP/
Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.
Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://github.com/Sung-Huan/ANNOgesic
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Proper citation: ANNOgesic (RRID:SCR_016326) Copy
https://www.jax.org/jax-mice-and-services
Supplier of mice for research purposes.
Proper citation: JAX Mice and Services (RRID:SCR_016408) Copy
Supplier of mice for research purposes. Provides technical services, model organisms, gene editing and decoding.
Proper citation: Shanghai Model Organisms Center (RRID:SCR_016407) Copy
Supplier of mice for research purposes.
Proper citation: National Resource Center for Mutant Mice (RRID:SCR_016406) Copy
Supplier of mice for research purposes.
Proper citation: Taconic Biosciences (RRID:SCR_016410) Copy
https://www.genomics.agilent.com/article.jsp?pageId=2100
Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MxPro QPCR (RRID:SCR_016375) Copy
http://django.nubic.northwestern.edu/fundo/
Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods.
Proper citation: FunDO (RRID:SCR_001725) Copy
http://caps.ncbs.res.in/stifdb2/
Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.
Proper citation: STIFDB (RRID:SCR_002131) Copy
http://pathway.gramene.org/gramene/ricecyc.shtml
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP.
Proper citation: Rice Metabolic Pathway Database (RRID:SCR_002128) Copy
http://www.homozygositymapper.org/
A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)
Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy
A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.
Proper citation: pSTIING (RRID:SCR_002045) Copy
https://enigma.lbl.gov/regprecise/
Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RegPrecise (RRID:SCR_002149) Copy
http://eyegene.ophthy.med.umich.edu/madeline/
Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review.
Proper citation: MADELINE (RRID:SCR_001979) Copy
http://giladlab.uchicago.edu/orthoExon/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms.
Proper citation: Primate Orthologous Exon Database (RRID:SCR_002065) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis.
Proper citation: Alignable Tight Genomic Cluster (RRID:SCR_001894) Copy
It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate.
Proper citation: PubGene (RRID:SCR_002119) Copy
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-335
Cell signaling pathways can be explored using PathFinder, the interactive, online graphical representation of cell signaling pathways. The user can use PathFinder to explore the relationships between different cell signaling pathway components while being presented with our high quality small molecules, antibodies, enzymes, siRNA for gene knockdown and qPCR components to aid them in their research.
Proper citation: Cell Signaling Pathways (RRID:SCR_002070) Copy
http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.
Proper citation: COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) Copy
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