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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | analysis service resource, data analysis service, production service resource, service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-09-12 01:01:42 | 114 | ||||||
|
Magic Resource Report Resource Website 500+ mentions |
Magic (RRID:SCR_006406) | MAGIC | data or information resource, database, service resource | Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. | gene expression, microarray, development stage, annotation, line, perturbation, gene, contrast, pathway, locus tag, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: ArrayExpress is related to: Plant Ontology is related to: Gene Ontology has parent organization: Ghent University; Ghent; Belgium |
PMID:24407224 | biotools:magic, OMICS_02206 | https://bio.tools/magic | SCR_006406 | MAGIC - MAize Gene expressIon Compendium, MAize Gene expressIon Compendium | 2026-09-12 01:01:42 | 709 | ||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | analysis service resource, data analysis service, production service resource, service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-09-12 01:01:42 | 3 | |||||
|
NCBI Epigenomics Resource Report Resource Website 10000+ mentions |
NCBI Epigenomics (RRID:SCR_006151) | Epigenomics | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. | genome-wide map, dna, histone, modification, epigenomic, genome, gold standard, gene mapping, gene amplification, genetic code, gene library, dna fingerprinting, chromatin, histone modification, dna methylation, dnaase footprinting, genome wide association study, gene expression |
is listed by: re3data.org is listed by: OMICtools is related to: Roadmap Epigenomics Project has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151643, OMICS_01848, r3d100010782 | https://doi.org/10.17616/R34K7J | http://www.ncbi.nlm.nih.gov/epigenomics | SCR_006151 | NCBI Epigenomic Gateway, National Center for Biotechnology Information Epigenomics, NCBI Epigenomic Hub | 2026-09-12 01:01:41 | 14631 | |||||
|
Consensus CDS Resource Report Resource Website 100+ mentions |
Consensus CDS (RRID:SCR_006729) | CCDS | data or information resource, database | Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly. | human genome sequence, human protein, mouse genome sequence, mouse protein, protein coding region, gene, genome sequence, genome, sequence, gene annotation, protein, gold standard |
is listed by: OMICtools is related to: Entrez Gene is related to: HomoloGene is related to: MapViewer is related to: VEGA has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: University of California at Santa Cruz; California; USA |
PMID:24217909 PMID:22434842 PMID:19498102 |
The community can contribute to this resource, Acknowledgement requested | nif-0000-02645, OMICS_01535 | http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi | SCR_006729 | CCDS Database, NCBI Consensus CDS protein set, NCBI CCDS Database | 2026-09-12 01:01:44 | 242 | |||||
|
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 500+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | analysis service resource, data analysis service, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-09-12 01:01:44 | 524 | |||||
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Haldanes Sieve Resource Report Resource Website 1+ mentions |
Haldanes Sieve (RRID:SCR_007178) | Haldane?s Sieve | blog, data or information resource, narrative resource | Blog discussing preprints in population and evolutionary genetics. | is listed by: OMICtools | OMICS_01714 | SCR_007178 | 2026-09-12 01:01:46 | 3 | ||||||||||
|
PRODORIC Resource Report Resource Website 50+ mentions |
PRODORIC (RRID:SCR_007074) | PRODORIC | data or information resource, database | Database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. The integrated approach provides information about molecular networks in prokaryotes with focus on pathogenic organisms. In detail this concerns: * transcriptional regulation (transcription factors and their DNA binding sites * signal transduction (two-component systems, phosphylation cascades) * protein interactions (complex formation, oligomerization) * biochemical pathways (chemical reactions) * other regulation events (e.g. codon usage, etc. ...) It aims to be a resource to model protein-host interactions and to be a suitable platform to analyze high-throughput data from proteomis and transcriptomics experiments (systems biology). Currently it mainly contains detailed information about operon and promoter structures including huge collections of transcription factor binding sites. If an appropriate number of regulatory binding sites is available, a position weight matrix (PWM) and a sequence logo is provided, which can be used to predict new binding sites. This data is collected manually by screening the original scientific literature. PRODORIC also handles protein-protein interactions and signal-transduction cascades that commonly occur in form of two-component systems in prokaryotes. Furthermore it contains metabolic network data imported from the KEGG database., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene regulation, transcription factor binding site, promoter structure, gene expression, genome, regulon, network, visualization, gene regulatory network, pathogen, transcriptional regulation, transcription factor, dna binding site, signal transduction, protein interaction, pathway, regulation, protein-protein interaction, signal-transduction cascade, operon, promoter, structure, position weight matrix, FASEB list |
is listed by: OMICtools is related to: KEGG has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
BMBF | PMID:18974177 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03343, OMICS_01872 | http://www.prodoric.de | SCR_007074 | Prokaryotic Database of Gene Regulation | 2026-09-12 01:01:45 | 57 | ||||
|
Arabidopsis Gene Regulatory Information Server Resource Report Resource Website 50+ mentions |
Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) | AGRIS | data or information resource, database | An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB). | gene regulatory, gene, arabidopsis thaliana, promoter sequence, target gene, transcription factor, FASEB list |
is listed by: OMICtools has parent organization: Ohio State University; Ohio; USA |
NSF | PMID:21059685 PMID:16524982 PMID:12820902 |
Free, Acknowledgement requested | OMICS_00548, nif-0000-02540 | SCR_006928 | 2026-09-12 01:01:44 | 53 | ||||||
|
COG Resource Report Resource Website 1000+ mentions |
COG (RRID:SCR_007139) | COG, COG Cluster, COG Function, COG Pathway | data or information resource, database | A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be. | ortholog, protein, cog, conserved protein sequence, unicellular cluster, genome, order, class, phyla, eukaryotic cluster, gold standard |
is listed by: OMICtools is related to: MLTreeMap is related to: ProOpDB is related to: Conserved Domain Database has parent organization: NCBI is parent organization of: Clusters of Orthologous Groups Analysis Ontology |
PMID:12969510 PMID:9381173 |
OMICS_01688, nif-0000-02672 | SCR_007139 | COG Database, Clusters of Orthologous Groups of proteins, COGs, COGs - Clusters of Orthologous Groups of proteins, COGs - Phylogenetic classification of proteins encoded in complete genomes, COG Cluster, COG Pathway, COG Function | 2026-09-12 01:01:46 | 1278 | |||||||
|
AthaMap Resource Report Resource Website 50+ mentions |
AthaMap (RRID:SCR_006717) | data or information resource, database | Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. | gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list |
is listed by: OMICtools is listed by: bio.tools has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
PMID:22800758 PMID:21177332 PMID:18842622 PMID:17148485 PMID:16922688 PMID:15980498 PMID:14681436 |
Free, Freely available | nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 | https://bio.tools/athamap | SCR_006717 | Arabidopsis thaliana Map | 2026-09-12 01:01:43 | 50 | ||||||
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Database of Poplar Transcription Factors Resource Report Resource Website 1+ mentions |
Database of Poplar Transcription Factors (RRID:SCR_007080) | DPTF | data or information resource, database | Database of collected known and predicted transcription factors (TF) of the black cottonwood tree, Populus trichocarpa. They have made extensive annotations, including similarity searches against major databases (Uniprot, RefSeq, EMBL, TRANSFAC et al) and EST expression information extraction from UniGene clusters and microarray expression, to provide comprehensive information for the putative TFs. In addition, multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Arabidopsis Transcription Factors (DATF), the Database of Rice Transcription Factors (DRTF) are included. | transcription factor |
is listed by: OMICtools is related to: PLANTTFDB has parent organization: Peking University; Beijing; China |
PMID:17392330 | Free, Acknowledgement requested | OMICS_00553 | SCR_007080 | 2026-09-12 01:01:45 | 7 | |||||||
|
GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | Generic Genome Browser | 2026-09-12 01:01:44 | 43 | ||||
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Next-Gen Sequencing Resource Report Resource Website |
Next-Gen Sequencing (RRID:SCR_007245) | Next-Gen Sequencing | blog, data or information resource, narrative resource | A working guide to the rapidly developing world of Next-Generation DNA sequencing, with an emphasis on bioinformatics. | is listed by: OMICtools | OMICS_01717 | SCR_007245 | 2026-09-12 01:01:46 | 0 | ||||||||||
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miRGator Resource Report Resource Website 50+ mentions |
miRGator (RRID:SCR_007793) | miRGator | data or information resource, database | Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets. | genome, functional annotation, microrna, expression profile, mir-seq, mirna-mrna target relation, expression correlation, FASEB list |
is listed by: OMICtools has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
Korean Rural Development Administration 20070401034010; Korean Ministry of Science and Technology ; Ministry of Education and Human Resources Development |
PMID:23193297 PMID:21062822 PMID:17942429 |
nif-0000-03136, OMICS_00363 | http://203.255.191.19/MEXWebApp/, http://genome.ewha.ac.kr/miRGator/miRGator.html | SCR_007793 | miRGator: an integrated system for functional annotation of microRNAs | 2026-09-12 01:01:52 | 55 | |||||
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Mutation Annotation and Genomic Interpretation Resource Report Resource Website |
Mutation Annotation and Genomic Interpretation (RRID:SCR_002800) | MAGI | analysis service resource, data analysis service, production service resource, service resource | A tool for annotating, exploring, and analyzing gene sets that may be associated with cancer. | mutation, interaction, transcript, copy number aberration, network |
uses: The Cancer Genome Atlas uses: HINT uses: HPRD - Human Protein Reference Database uses: Pfam uses: SMART uses: Conserved Domain Database is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
Cancer | NSF ; NIH ; Brown University; Rhode Island; USA |
Free, Freely available, Available for download | OMICS_06145 | SCR_002800 | MAGI - A tool for Mutation Annotation and Genomic Interpretation | 2026-09-12 01:01:26 | 0 | |||||
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Autophagy Database Resource Report Resource Website 10+ mentions |
Autophagy Database (RRID:SCR_002671) | Autophagy DB, AutophagyDB | data or information resource, database | Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes. | autophagy, protein, homolog, ortholog, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:20972215 | Free, Available for download, Freely available | OMICS_03306, biotools:the_autophagy_database, r3d100012565 | https://bio.tools/the_autophagy_database, https://doi.org/10.17616/R3J786 | SCR_002671 | 2026-09-12 01:01:26 | 22 | |||||
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Greengenes Resource Report Resource Website 1000+ mentions |
Greengenes (RRID:SCR_002830) | data or information resource, database | Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, rrna, 16s rrna, gene, dna, rna, chimera, alignment, taxonomic classification, taxonomy, FASEB list |
is listed by: OMICtools is listed by: re3data.org is listed by: Human Microbiome Project has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy contract DE-AC02-05CH11231 | PMID:16820507 | Free, Freely available | OMICS_01512, r3d100010549, nif-0000-02927 | http://greengenes.lbl.gov, https://doi.org/10.17616/R36C8G | SCR_002830 | 2026-09-12 01:01:26 | 3162 | ||||||
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DOMINE: Database of Protein Interactions Resource Report Resource Website 1+ mentions |
DOMINE: Database of Protein Interactions (RRID:SCR_002399) | DOMINE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014) | domain-domain interaction, prediction, protein domain, interaction, protein domain interaction, protein, domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Pfam has parent organization: University of Texas at Dallas; Texas; USA |
PMID:21113022 PMID:17913741 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01906, nif-0000-02758, biotools:domine | https://bio.tools/domine | SCR_002399 | Database of Protein Domain Interactions | 2026-09-12 01:01:25 | 2 | |||||
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DBTBS Resource Report Resource Website 10+ mentions |
DBTBS (RRID:SCR_002345) | DBTBS | data or information resource, database | Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins. | gene, gene regulatory network, transcription factor binding site, transcription factor, regulated operon, motif, promoter, motif conservation |
is listed by: OMICtools has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:17962296 PMID:14681362 PMID:11125112 |
Acknowledgement requested | nif-0000-02736, OMICS_01859 | SCR_002345 | DBTBS: a database of Bacillus subtilis promoters and transcription factors., DBTBS: a database of Bacillus subtilis promoters and transcription factors | 2026-09-12 01:01:25 | 34 |
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