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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HOCOMOCO Resource Report Resource Website 100+ mentions |
HOCOMOCO (RRID:SCR_005409) | HOCOMOCO | database, data or information resource | A comprehensive collection of human transcription factor binding sites models. DNA sequences of TF binding regions obtained by both pregenomic and high-throughput methods were collected from existing databases and other public data. The ChIPMunk software was used to construct positional weight matrices. Four motif discovery strategies were tested based on different motif shape priors including flat and periodic priors associated with DNA helix pitch. A quality rating was manually assigned to each model based on known binding preferences. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs. In any case only one model per TF was selected unless there was additional evidence for two distinct binding models or different stable modes of dimerization. All TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs. | transcription factor, binding model, model, binding, FASEB list |
is listed by: OMICtools has parent organization: Russian Academy of Sciences; Moscow; Russia |
PMID:23175603 | Acknowledgement requested | OMICS_00537 | SCR_005409 | Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models, Homo Sapiens Comprehensive Model Collection, Homo Sapiens Comprehensive Model Collection of transcription factor binding models | 2026-08-08 12:04:03 | 461 | ||||||
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footprintDB Resource Report Resource Website 10+ mentions |
footprintDB (RRID:SCR_005368) | footprintDB | database, data or information resource | Database with 2797 unique DNA-binding proteins (mostly transcription factors, TFs), 4196 Position Weight Matrices (PWMs) and 13161 DNA Binding Sites extracted from the literature and other repositories. The binding interfaces of (most) proteins in the database are inferred from the collection of protein-DNA complexes described in 3D-footprint. The database predicts transcription factors which bind a specific DNA site or motif and DNA motifs or sites likely to be recognized by a specific DNA-binding protein. | transcription factor, dna motif, dna, motif, dna-binding protein, position weight matrix, protein |
is listed by: OMICtools has parent organization: Spanish National Research Council; Madrid; Spain |
Free | OMICS_00535 | SCR_005368 | 2026-08-08 12:04:03 | 10 | ||||||||
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ChIPBase Resource Report Resource Website 100+ mentions |
ChIPBase (RRID:SCR_005404) | ChIPBase | database, data or information resource | A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chip-seq, gene, rna, microrna, long non-coding rna, non-coding, transcription factor binding site, protein, transcriptional regulation, annotation, regulatory element, transcription factor, genome, network, FASEB list |
is listed by: OMICtools has parent organization: Sun Yat-sen University; Guangdong; China |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00527 | SCR_005404 | 2026-08-08 12:03:52 | 145 | ||||||||
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SKIPPY Resource Report Resource Website 1+ mentions |
SKIPPY (RRID:SCR_005430) | SKIPPY | analysis service resource, data analysis service, production service resource, service resource | A Web-based tool that allows users to input a set of exonic variants to score them for a number of features (such as changes in splicing regulatory elements) that have been shown to be predictive of known genome variations that cause exon skipping or activation of ectopic splice sites. In this way, variants can be either prioritized for further splicing-based functional analysis or the results can be used as further genomic evidence in cases in which the causative variant is already known. | exonic variant, splicing, genome variation, coding variant |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
PMID:20158892 | OMICS_02258 | SCR_005430 | SKIPPY - A Tool for the Detection of Exonic Variants that Modulate Splicing | 2026-08-08 12:03:52 | 2 | |||||||
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TOBFAC Resource Report Resource Website 1+ mentions |
TOBFAC (RRID:SCR_005423) | TOBFAC | database, data or information resource | Database of transcription factor sequences from a single plant species (over 2,500 genes). It is possible to search: # 1,159,022 gene-space sequence reads (GSRs) obtained by methylation filtering from the Tobacco Genome Initiative (TGI). # The DFCI Tobacco Gene Index (Release 4.0 July 5, 2008) that contains 163,524 tobacco EST sequences and 2,288 expressed transcripts (ETs). # The complete TOBFAC database of tobacco transcription factors. It is also possible to search multiple libraries in a single search. They have incorporated tools for downloading all of the sequences from the blast results and also a contig tool to assemble any or all of the resulting sequences. They are also improving the TOBFAC sequences by extending the original contigs using a contig extension tool designed by Ryan Thompson. This has allowed them to refine the predicted genes. These will be updated on a gene family basis as the improved data become available. | transcription factor | is listed by: OMICtools | PMID:18221524 | Free | OMICS_00564 | SCR_005423 | TOBFAC: The database of tobacco transcription factors | 2026-08-08 12:04:03 | 8 | ||||||
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miRdSNP Resource Report Resource Website 10+ mentions |
miRdSNP (RRID:SCR_005303) | miRdSNP | database, data or information resource | A database of manually curated dSNPs on the 3''UTRs of human genes from available publications in PubMed. The advanced web interface allows users to perform proximity searches between miRNA target sites and dSNPs by gene name, miRbase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites. The web interface displays detailed sequence views showing the relationship between dSNPs, miRNA target sites, and SNPs. An interactive visualization tool shows the chromosomal distribution of dSNPs, miRNA target sites (from TargetScan), and SNPs. miRdSNP provides a comprehensive data source of dSNPs and robust tools to capture their spacial relationship with miRNA target sites on the 3''UTRs of human genes. miRdSNP enables researchers to further explore the molecular mechanism of gene dysregulation for dSNPs at posttranscriptional level. |
is listed by: OMICtools has parent organization: University at Buffalo; New York; USA |
PMID:22276777 | Free, Public | OMICS_00389 | SCR_005303 | miRdSNP - a database of disease-associated SNPs and microRNA target sites on 3''UTRs of human genes | 2026-08-08 12:04:03 | 24 | |||||||
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StSNP Resource Report Resource Website 1+ mentions |
StSNP (RRID:SCR_005417) | StSNP | analysis service resource, data analysis service, production service resource, service resource | A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00138, biotools:stsnp | https://bio.tools/stsnp | SCR_005417 | Structure SNP | 2026-08-08 12:04:03 | 3 | |||||||
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Tractor db Resource Report Resource Website 1+ mentions |
Tractor db (RRID:SCR_005610) | Tractor db | database, data or information resource | Database of computationally predicted Transcription Factors and binding sites in gamma-proteobacterial genomes. The user may browse a map containing all known E. coli transcription factors and regulatory interactions that connect them, and retrieve information on the conservation of each regulatory interaction across the 30 organisms included in the database. Downloading the information is straightforward, and navigation tabs added to dynamic pages ease navigation between the five interfaces of the database. The original prediction approach, based on the representation of binding sites through statistical models was complemented by a new approach that uses known E. coli regulatory sites as the basis for a pattern matching search of regulatory sites. The use of both approaches together resulted in a more intensive exploration of the sequence space of each regulator's binding site. These data should aid researchers in the design of microarray experiments and the interpretation of their results. They should also facilitate studies of Comparative Genomics of the regulatory networks of this group of organisms. | gamma-proteobacterial genome, transcription factor binding site, transcription factor, regulatory network, microarray, comparative genomicis, genome |
is listed by: OMICtools has parent organization: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil has parent organization: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil |
PMID:17088283 | OMICS_01863, nif-0000-03574 | http://www.bioinfo.cu/Tractor_DB, http://www.tractor.lncc.br, http://www.ccg.unam.mx/tractorDB | SCR_005610 | Tractor_DB | 2026-08-08 12:03:53 | 3 | ||||||
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PRINSEQ Resource Report Resource Website 1000+ mentions |
PRINSEQ (RRID:SCR_005454) | PRINSEQ | analysis service resource, data analysis service, production service resource, service resource | A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, data analysis, genomic sequence data, metagenomic sequence data, summary, perl, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: San Diego State University; California; USA |
PMID:21278185 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01068, biotools:prinseq | http://prinseq.sourceforge.net, https://bio.tools/prinseq | SCR_005454 | PReprocessing and INformation of SEQuences, preprocessing and information of sequences | 2026-08-08 12:04:03 | 1199 | |||||
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PIE the search Resource Report Resource Website 1+ mentions |
PIE the search (RRID:SCR_005296) | PIE | database, data or information resource, service resource | A web service to extract Protein-protein interaction (PPI)-relevant articles from MEDLINE that provides protein interaction information (PPI) articles for biologists, baseline system performance for bio-text mining researchers and a compact PubMed-search environment for PubMed users. It accepts PubMed input formats including All Fields, Author, Journal, MeSH Terms, Publication Date, Title, and Title/Abstract with Boolean operations (AND, OR, and NOT). However, the output is the list of articles prioritized by PPI confidence rates. Some words (mostly gene/protein names) which contributed for PPI prediction are underlined and linked to Entrez or Entrez Gene. Even though our system focuses on a PubMed search environment, it also provides a CGI access for bio-text mining researchers. Using the CGI program, a list of PubMed IDs can be obtained as a query result, thus it can be utilized as a baseline system performance. PIE the search is based on a winning approach in the BioCreative III ACT competition (BC3)1. For input queries, MEDLINE articles are first retrieved through the PubMed service. PPI scores are calculated for the retrieved articles, and the articles are re-ranked based on scores. To effectively capture PPI patterns from biomedical literature, their approach utilizes both word and syntactic features for machine learning classifiers. Dependency parsing, gene mention tagging, and term-based features are utilized along with a Huber classifier. | protein interaction, protein-protein interaction, protein, interaction |
is listed by: OMICtools is related to: PubMed is related to: MEDLINE has parent organization: NCBI |
PMID:22199390 PMID:22151252 |
OMICS_01191 | SCR_005296 | Protein Interaction information Extraction the search | 2026-08-08 12:03:51 | 1 | |||||||
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TopoSNP Resource Report Resource Website 1+ mentions |
TopoSNP (RRID:SCR_005572) | TopoSNP | database, data or information resource | A topographic database for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins. These include disease- associated nsSNPs derived from the Online Mendelian Inheritance in Man (OMIM) database and other nsSNPs derived from dbSNP, a resource at the National Center for Biotechnology Information that catalogs SNPs. TopoSNP further classifies each nsSNP site into three categories based on their geometric location: those located in a surface pocket or an interior void of the protein, those on a convex region or a shallow depressed region, and those that are completely buried in the interior of the protein structure. These unique geometric descriptions provide more detailed mapping of nsSNPs to protein structures. It also includes relative entropy of SNPs calculated from multiple sequence alignment as obtained from the Pfam database (a database of protein families and conserved protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW. These structural and conservational data can be useful for studying whether nsSNPs in coding regions are likely to lead to phenotypic changes. TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data. | visualization, disease, non-disease, non-synonymous single nucleotide polymorphism, topographic mapping, single nucleotide polymorphism, 3d structure, protein, protein structure, coding region, entropy |
is listed by: OMICtools is related to: OMIM is related to: dbSNP is related to: Pfam is related to: Clustal W2 has parent organization: University of Illinois at Chicago; Illinois; USA |
NSF DBI0133856; NSF DBI0078270; NSF MCB998008; NIGMS GM68958 |
PMID:14681472 | nif-0000-03570, OMICS_00191 | SCR_005572 | topographic mapping of Single Nucleotide Polymorphism | 2026-08-08 12:03:53 | 5 | ||||||
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CyMATE Resource Report Resource Website 50+ mentions |
CyMATE (RRID:SCR_005442) | CyMATE | analysis service resource, data analysis service, production service resource, service resource | A web application that allows you to perform a quick and comprehensive methylation analysis of cytosine sites in DNA sequences. |
is listed by: OMICtools has parent organization: Gregor Mendel Institute has parent organization: Vienna University of Technology; Vienna; Austria |
PMID:17559516 | OMICS_00597 | http://www.gmi.oeaw.ac.at/research-groups/cymate/cymate/ | SCR_005442 | Cytosine Methylation Analysis Tool for Everyone | 2026-08-08 12:03:52 | 70 | |||||||
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TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | analysis service resource, data analysis service, production service resource, service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-08-08 12:04:04 | 5 | ||||||
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SPOT - Biological prioritization after a SNP association study Resource Report Resource Website 500+ mentions |
SPOT - Biological prioritization after a SNP association study (RRID:SCR_005193) | SPOT | analysis service resource, data analysis service, production service resource, service resource | A web-based tool for using biological databases to prioritize single nucleotide polymorphisms (SNPs) after a genome-wide association study (GWAS). The site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. Users can specify candidate genes or genomic regions with custom levels of prioritization. The results can be downloaded or viewed in the browser where users can interactively explore the details of each SNP, including graphical representations of the genomic information network (GIN) method. For investigators interested in incorporating biological databases into a post-GWAS SNP selection strategy, the SPOT web tool is an easily implemented and flexible solution. | single nucleotide polymorphism, genome-wide association study, linkage disequilibrium, gene, genomic region, p-value, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:20529875 | biotools:spot, OMICS_00189 | https://bio.tools/spot | SCR_005193 | 2026-08-08 12:04:02 | 512 | |||||||
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MethylomeDB Resource Report Resource Website 1+ mentions |
MethylomeDB (RRID:SCR_005583) | MethylomeDB | database, data or information resource | A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database. | brain, dna methylation, dorsal lateral prefrontal cortex, ventral prefrontal cortex, auditory cortex, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Columbia University; New York; USA |
NIH ; NHGRI HG002915; NIMH MH074118 |
PMID:22140101 | OMICS_01843, nlx_146210, biotools:methylomedb | https://bio.tools/methylomedb | SCR_005583 | MethylomeDB - the Brain Methylome Database, Brain Methylome Database | 2026-08-08 12:04:00 | 1 | |||||
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Unified Human Interactome Resource Report Resource Website 10+ mentions |
Unified Human Interactome (RRID:SCR_005805) | UniHI | database, data or information resource | A database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks. | molecular interaction network, interactome, protein, protein interaction network, protein interaction, pathway, function, visualization, protein-protein interaction, transcriptional regulatory interaction, network |
is listed by: OMICtools has parent organization: University of Algarve; Faro; Portugal |
PMID:24214987 PMID:22218860 PMID:18984619 PMID:17158159 |
Public, Non-commercial | OMICS_01911, nif-0000-03609 | http://www.mdc-berlin.de/unihi | SCR_005805 | 2026-08-08 12:04:01 | 20 | ||||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-08-08 12:04:00 | 36 | |||||
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OntoVisT Resource Report Resource Website 1+ mentions |
OntoVisT (RRID:SCR_005674) | OntoVisT | database, data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. Web based ontological visualization tool for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery. | ontology, visualization, web service, gene ontology, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, dag hierarchical form, dag, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: OBO has parent organization: Jawaharlal Nehru University; New Delhi; India |
Council of Scientific and Industrial Research; New Delhi; India ; Jawaharlal Nehru University; New Delhi; India ; Department of Biotechnology |
PMID:21738333 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02274, nlx_149113 | SCR_005674 | OntoVisT: A General purpose Ontological Visualization Tool | 2026-08-08 12:03:54 | 1 | |||||
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REViGO Resource Report Resource Website 1000+ mentions |
REViGO (RRID:SCR_005825) | REViGO | analysis service resource, data analysis service, production service resource, service resource | Web server that summarizes lists of Gene Ontology terms by removing redundant terms and visualizing the remaining ones in scatterplots, interactive graphs, treemaps, or tag clouds. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene ontology, visualization, statistical analysis, ontology or annotation visualization |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Rudjer Boskovic Institute; Zagreb; Croatia |
PMID:21789182 PMID:20585573 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02283, nlx_149332 | SCR_005825 | Reduce + Visualize Gene Ontology, REViGO - Reduce Visualize Gene Ontology, REViGO - Reduce & Visualize Gene Ontology, REViGO - Reduce and Visualize Gene Ontology, REViGO - Reduce + Visualize Gene Ontology | 2026-08-08 12:04:06 | 2430 | ||||||
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SNPsandGO Resource Report Resource Website 50+ mentions |
SNPsandGO (RRID:SCR_005788) | SNPs&GO | analysis service resource, data analysis service, production service resource, service resource | A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans. | prediction, protein, mutation, disease, single nucleotide polymorphism, bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Bologna; Bologna; Italy |
PMID:19514061 | biotools:snps_go, OMICS_02219 | https://bio.tools/snps_go | SCR_005788 | SNPs and GO | 2026-08-08 12:04:00 | 61 |
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