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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | database, data or information resource, service resource | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-08-08 12:03:42 | 459 | |||||
|
MapViewer Resource Report Resource Website 100+ mentions |
MapViewer (RRID:SCR_003092) | Map Viewer | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. | genome, mapping, sequencing, chromosome |
is listed by: OMICtools is related to: NCBI Genome is related to: Consensus CDS has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00921, nif-0000-03103 | SCR_003092 | Entrez Map Viewer, NCBI Map Viewer | 2026-08-08 12:03:55 | 244 | |||||||
|
e-PCR Resource Report Resource Website 10+ mentions |
e-PCR (RRID:SCR_003082) | e-PCR | analysis service resource, data analysis service, production service resource, service resource | Web tool that identifies sequence tagged sites (STSs) within DNA sequences. Using e-PCR, you can search for sub-sequences that closely match the PCR primers and have the correct order, orientation, and spacing. The software may also be downloaded to run locally. | sequence tagged site, dna sequence, reverse, forward |
is listed by: OMICtools is listed by: Debian has parent organization: NCBI |
PMID:15215361 PMID:9149949 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02345 | https://sources.debian.org/src/ncbi-epcr/ | http://www.ncbi.nlm.nih.gov/sutils/e-pcr | SCR_003082 | Electronic PCR, Electronic PCR (e-PCR) | 2026-08-08 12:03:50 | 13 | ||||
|
Type-III-Secretion-System related database Resource Report Resource Website |
Type-III-Secretion-System related database (RRID:SCR_002941) | T3DB | database, data or information resource | Database aimed to annotate all bacterial Type III Secretion System (T3SS) related structure, effector, regulator, and auxiliary genes. | type iii secretion system, gene, protein, ortholog |
is listed by: OMICtools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:22545727 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05160 | SCR_002941 | T3SS-related Database | 2026-08-08 12:03:50 | 0 | ||||||
|
PlantProm DB Resource Report Resource Website 1+ mentions |
PlantProm DB (RRID:SCR_003359) | PlantProm | database, data or information resource | Annotated, non-redundant database of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s) (TSS) from various plant species. It contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively (April 2014). This DB presents the published promoter sequences with TSS(s) determined by direct experimental approaches and therefore serves as the most accurate source for development of computational promoter prediction tools. | proximal promoter sequence, rna polymerase ii, transcription start site, promoter, monocot, dicot, dna sequence, taxonomy, promoter type, nucleotide frequency matrix, nucleotide composition, motif, transcription, regulatory element |
is listed by: OMICtools has parent organization: University of London; London; United Kingdom |
Pakistan European Union | PMID:12519961 | Free, Available for download, Freely available | nif-0000-03308, OMICS_01875 | http://www.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom | http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom | SCR_003359 | Plant Promoter Database, PlantProm DB | 2026-08-08 12:03:43 | 8 | |||
|
PPDB: Plant Promoter Database Resource Report Resource Website |
PPDB: Plant Promoter Database (RRID:SCR_003395) | PPDB | database, data or information resource | A plant promoter database that provides information on transcription start sites (TSSs), core promoter structure and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles. | gene, transcription start site, promoter structure, promoter, regulatory element group, homolog |
is listed by: OMICtools has parent organization: Gifu University; Gifu; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:24194597 PMID:17947329 |
Free, Available for download, Freely available | nif-0000-03329, OMICS_01874 | http://ppdb.gene.nagoya-u.ac.jp/cgi-bin/index.cgi | SCR_003395 | Plant Promoter Database | 2026-08-08 12:03:43 | 0 | ||||
|
NYCE Resource Report Resource Website |
NYCE (RRID:SCR_003144) | NYCE | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that predicts subcellular location (either Nuclear, Nucleo-cytoplasmic, Cytoplasmic or Extracellular) of eukaryotic proteins using the predicted exposure value of their amino acids. | subcellular localization, protein, amino acid, eukaryote |
is listed by: OMICtools has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
PMID:24283794 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01630 | SCR_003144 | 2026-08-08 12:03:51 | 0 | |||||||
|
Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | analysis service resource, data analysis service, production service resource, service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/, http://www.gepas.org/, http://babelomics3.bioinfo.cipf.es | http://www.babelomics.org | SCR_002969 | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-08-08 12:03:42 | 138 | |||
|
ResponseNet Resource Report Resource Website 1+ mentions |
ResponseNet (RRID:SCR_003176) | ResponseNet | analysis service resource, data analysis service, production service resource, service resource | WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming. | interactome, gene, protein, signaling pathway, signaling, regulatory, pathway, regulatory pathway, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23761447 PMID:21576238 |
Free, Freely available | biotools:responsenet, OMICS_01562 | https://bio.tools/responsenet | http://netbio.bgu.ac.il/respnet/ | SCR_003176 | 2026-08-08 12:03:43 | 4 | |||||
|
iLoc-Animal Resource Report Resource Website 1+ mentions |
iLoc-Animal (RRID:SCR_003173) | iLoc-Animal | analysis service resource, data analysis service, production service resource, service resource | Data analysis service for predicting subcellular localization of animal proteins with single or multiple sites. | subcellular localization, animal, protein | is listed by: OMICtools | PMID:23370050 | Free, Freely available | OMICS_01623 | https://pubs.rsc.org/en/content/articlelanding/2013/mb/c3mb25466f | SCR_003173 | iLoc-Animal: Predicting subcellular localization of animal proteins with single or multiple sites | 2026-08-08 12:03:55 | 6 | |||||
|
Hapmix Resource Report Resource Website 50+ mentions |
Hapmix (RRID:SCR_004203) | HAPMIX | software resource, software application, source code | Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, admixed, population, genotype, single nucleotide polymorphism, ancestry, chromosomal segment, snp array |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Harvard Medical School; Massachusetts; USA |
NHGRI U01-HG004168; NHLBI R01-HL087699 |
PMID:19543370 | Restricted | nlx_22768, OMICS_02082 | http://www.hsph.harvard.edu/faculty/alkes-price/software/, http://www.stats.ox.ac.uk/~myers/software.html, https://reich.hms.harvard.edu/software | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004203 | 2026-08-08 12:03:57 | 52 | ||||
|
FIDEA Resource Report Resource Website 1+ mentions |
FIDEA (RRID:SCR_004187) | FIDEA | analysis service resource, data analysis service, production service resource, service resource | A web server for the functional interpretation of differential expression analysis. It can: * Calculate overrepresentation statistics using KEGG, Interpro, Gene Ontology Molecular Function, Gene Ontology Biological Process, Gene Ontology Cellular Component and GoSlim classifications; * Analyze down-regulated and up-regulated DE genes separately or together as a single set; * Provide interactive graphs and tables that can be modified on the fly according to user defined parameters; the user can set a fold change filter and interactively see the effects on the gene set under examination; * Output publication-ready plot of the graph; * Compare the results of several experiments in any combination. |
is listed by: OMICtools has parent organization: Sapienza University of Rome; Rome; Italy |
PMID:23754850 | Public, Free, Acknowledgement requested | OMICS_01539 | SCR_004187 | Functional Interpretation of Differential Expression Analysis | 2026-08-08 12:03:53 | 9 | |||||||
|
Factorbook Resource Report Resource Website 10+ mentions |
Factorbook (RRID:SCR_004086) | Factorbook | database, data or information resource | A Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. | transcription factor, genome, transcription factor binding region, chip-seq |
is listed by: OMICtools is related to: ENCODE |
PMID:22955990 | OMICS_00533 | SCR_004086 | 2026-08-08 12:03:44 | 22 | ||||||||
|
My Cancer Genome Resource Report Resource Website 100+ mentions |
My Cancer Genome (RRID:SCR_004140) | MCG | database, data or information resource | A freely available online personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers that gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. It is a one-stop tool that matches tumor mutations to therapies, making information accessible and convenient for busy clinicians. | genome, disease, genome, medicine, clinical trial, mutation, therapy, FASEB list |
is listed by: OMICtools has parent organization: Vanderbilt University; Tennessee; USA |
Cancer, Tumor | PMID:32483629 | OMICS_01552 | SCR_004140 | MyCancerGenome.org | 2026-08-08 12:03:57 | 114 | ||||||
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Human DNA Polymerase Gamma Mutation Database Resource Report Resource Website 10+ mentions |
Human DNA Polymerase Gamma Mutation Database (RRID:SCR_004722) | Human DNA Polymerase Gamma Mutation Database | database, data or information resource | Database that lists all known mutations in the coding region of the POLG gene and describes the associated disease. Human DNA polymerase is composed of two subunits, a 140 kDa catalytic subunit encoded by the POLG on chromosome 15q25, and a 55kDa accessory subunit encoded by the POLG2 gene on chromosome 17q23-24. A number of mutations have been mapped to the gene for the catalytic subunit of DNA polymerase, POLG, and found to be associated with mitochondrial diseases. The nucleotide changes are numbered from the initiation Methionine codon and are based on the cDNA (accession U60325.1) and gene sequence (accession AF497906.1). | mutation, polg, gene, dna polymerase, FASEB list |
is listed by: OMICtools has parent organization: National Institute of Environmental Health Sciences |
Mitochondrial disease | Free | OMICS_01639, nlx_71693 | SCR_004722 | 2026-08-08 12:03:48 | 39 | |||||||
|
Nu-OSCAR Resource Report Resource Website 1+ mentions |
Nu-OSCAR (RRID:SCR_004513) | OSCAR | analysis service resource, data analysis service, production service resource, service resource | Software tool to identify binding sites of known transcription factors on promoter regions. The algorithm is based on one-class support vector machine (One-class SVM). OSCAR uses the sequential composition of known binding sites, and further incorporates the locational preferences of binding events. Nu-OSCAR (Nucleosome-Occupancy Study for Cis-elments Accurate Recognition) is a program that can be used to identify binding sites of known transcription factors, which further incorporates nucleosome occupancy around sites on promoter regions, thereby improving the accuracy of prediction. The derivation of the the algorithm is based on a biophysical view of interactions between protein factors and nucleosome DNA. |
is listed by: OMICtools has parent organization: Tsinghua University; Beijing; China |
OMICS_00507, nlx_49691, SCR_010892 | SCR_004513 | One-class SVM for Cis-elements Accurate Recognition, Nucleosome-Occupancy Study for Cis-elments Accurate Recognition | 2026-08-08 12:03:47 | 4 | |||||||||
|
UniGene Resource Report Resource Website 1000+ mentions |
UniGene (RRID:SCR_004405) | UniGene | database, data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters. | colleciton, data, information, organized, view, transcriptome, locus, protein, similarity, gene, expression, |
is used by: Rank Rank Hypergeometric Overlap is listed by: OMICtools is listed by: re3data.org is related to: ProbeMatchDB 2.0 is related to: Bgee: dataBase for Gene Expression Evolution is related to: GeneSpeed- A Database of Unigene Domain Organization has parent organization: NCBI works with: Digital Differential Display (DDD) |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_41571, OMICS_01663, r3d100010774 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene, https://doi.org/10.17616/R35G7T | SCR_004405 | NCBI UniGene, Organized View of the Transcriptome, UniGene | 2026-08-08 12:03:58 | 1153 | ||||||
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GEN Resource Report Resource Website |
GEN (RRID:SCR_012901) | data or information resource, narrative resource | News source including the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization. | is listed by: OMICtools | OMICS_01730 | SCR_012901 | Genetic Engineering & Biotechnology News, Genetic Engineering and Biotechnology News | 2026-08-08 12:05:19 | 0 | ||||||||||
|
mothur Resource Report Resource Website 5000+ mentions |
mothur (RRID:SCR_011947) | standalone software, software resource, software application | An open-source software package for describing and comparing microbial communities. It incorporates the functionality of a number of computational tools, calculators, and visualization tools. | microbiome, microbial ecology, open source, bioinformatics, standalone software |
is used by: Nephele is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian |
DOI:10.1128/AEM.01541-09 | Open source | OMICS_01518 | https://github.com/mothur/mothur/releases/tag/v1.38.1.1, https://sources.debian.org/src/mothur/ | SCR_011947 | 2026-08-08 12:05:08 | 6270 | |||||||
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BIKA Resource Report Resource Website 1+ mentions |
BIKA (RRID:SCR_011828) | BIKA | software resource, service resource | Open Source laboratory information management systems. | is listed by: OMICtools | GNU Affero General Public License | OMICS_01003 | SCR_011828 | 2026-08-08 12:05:15 | 2 |
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