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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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modENCODE Resource Report Resource Website 100+ mentions |
modENCODE (RRID:SCR_006206) | modENCODE | production service resource, data analysis service, service resource, analysis service resource, data or information resource, data set | A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets. | epigenomics, epigenetics, genomics, functional element, model organism, genome, copy number variation, gene structure, genome sequence, histone modification, histone replacement, chromatin binding site, expression profiling, replication, transcription factor binding site, transcription factor, binding site, chromatin, rna, expression profiling, regulatory network, mrna, ncrna, dna replication, genotype |
is related to: ENCODE is related to: Encode |
NHGRI | PMID:19536255 | Public, With some restrictions on its use for 9 months following publication, Acknowledgement requested | nlx_151752 | SCR_006206 | NHGRI model organism ENCyclopedia Of DNA Elements, National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements, model organism ENCyclopedia Of DNA Elements | 2026-08-03 09:32:56 | 255 | |||||
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Cscan Resource Report Resource Website 1+ mentions |
Cscan (RRID:SCR_006756) | Cscan | production service resource, data analysis service, data or information resource, database, analysis service resource, service resource | Data resource that includes a large collection of genome-wide ChIP-Seq experiments performed on transcription factors (TFs), histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. | regulator, gene, genome-wide chip-seq, chip-seq, gene, genome | is listed by: OMICtools | PMID:22669907 | Free | OMICS_00529 | SCR_006756 | 2026-08-03 09:33:14 | 4 | |||||||
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OpenWorm Resource Report Resource Website 10+ mentions |
OpenWorm (RRID:SCR_014650) | simulation software, software resource, software application, web application | 3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders. | simulation, model, web application, web browser, c elegans, nematode, worm, roundworm, open source, 3d, dissect, anatomy, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: WormBase is hosted by: GitHub |
PMID:25404913 DOI:10.3389/fncom.2014.00137 |
Open source, Code is available on GitHub, Available on the App Store | SCR_014984, biotools:OpenWorm | https://bio.tools/OpenWorm | SCR_014650 | OpenWorm Browser, Open Worm | 2026-08-03 09:35:49 | 21 | ||||||
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Caenorhabditis elegans Natural Diversity Resource (CeNDR) Resource Report Resource Website 10+ mentions |
Caenorhabditis elegans Natural Diversity Resource (CeNDR) (RRID:SCR_014958) | CeNDR | biomaterial supply resource, material resource, organism supplier | Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery. | c. elegans, caenorhabditis elegans, strains, n2, roundworm, nematode, gene analysis, organism supplier, portal | has parent organization: Northwestern University; Illinois; USA | American Cancer Society Research Scholar Award ; Amazon Web Services Research Grant ; Weinberg College of Arts and Sciences starter innovation award ; Northwestern University Start-up Funds ; NIGMS R01GM107227; NSF DGE-1324585 |
PMID:27701074 | Available to the research community | SCR_014958 | Caenorhabditis elegans Natural Diversity Resource | 2026-08-03 09:35:41 | 22 | ||||||
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GeneInfoViz Resource Report Resource Website |
GeneInfoViz (RRID:SCR_005680) | GeneInfoViz | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool | gene network, gene ontology, visualization, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:15724283 | Free for academic use | nlx_149121 | SCR_005680 | GeneInfoViz: Constructing and Visualizing Gene Relation Networks | 2026-08-03 09:32:45 | 0 | ||||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | software resource, data processing software, software application, data analysis software | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-08-03 09:34:09 | 8 | |||||
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SL-quant Resource Report Resource Website 1+ mentions |
SL-quant (RRID:SCR_016205) | SLQ | sequence analysis software, software application, data processing software, data analysis software, software resource | Source code for a bash pipeline that quantifies splice-leader (SL) trans-splicing events by genes in the nematode C. elegans. It is designed to work downstream of read mapping and takes the reads left unmapped as primary input. | RNA-seq, trans-splicing, pipeline, c elegans, bash, nematode, read, mapping, gene |
requires: cutadapt requires: SAMTOOLS requires: HISAT2 requires: BEDTools requires: Picard requires: featureCounts |
FNRS-FRIA | Free, Available for download | SCR_016205 | 2026-08-03 09:36:39 | 1 | ||||||||
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WormBase Resource Report Resource Website 1000+ mentions |
WormBase (RRID:SCR_003098) | WB, WB REF, WP | data repository, data or information resource, database, storage service resource, service resource | Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases. | RIN, Resource Information Network, catalog, database, blast, genomic sequence, gene prediction, orthology assignment, gene function, ortholog, roundworm, geneotype, phenotype, gene mapping, genomics, gene expression, transposon family, c elegans, wormmart, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: AmiGO is related to: GBrowse is related to: Textpresso is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: C. elegans Gene Knockout Consortium is related to: NIH Data Sharing Repositories is related to: UniParc at the EBI is related to: UniParc is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Cold Spring Harbor Laboratory has parent organization: Washington University in St. Louis; Missouri; USA has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: C. elegans Development Vocabulary is parent organization of: C. elegans Gross Anatomy Vocabulary is parent organization of: C. elegans Phenotype Vocabulary is parent organization of: OpenWorm works with: A plasmid Editor is organization facet of: Alliance of Genome Resources |
NHGRI ; NIH Blueprint for Neuroscience Research ; MRC ; BBSRC ; NHGRI U41 HG002223; NIHGRI P41 HG02223 |
PMID:24194605 PMID:19910365 PMID:17991679 PMID:15608221 |
nif-0000-00053, OMICS_01664, r3d100010424 | http://www.wormbase.org/#01-23-6, https://doi.org/10.17616/R3089Z | SCR_003098 | , WB, Worm Base, WB REF, WP | 2026-08-03 09:32:10 | 1825 | |||||
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GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | production service resource, data analysis service, web service, analysis service resource, data access protocol, service resource, software resource | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, 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 is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-08-03 09:33:18 | 348 | ||||
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GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | production service resource, data analysis service, software application, analysis service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Harvard University; Cambridge; United States |
PMID:12724301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149203 | http://genemerge.cbcb.umd.edu/ | SCR_005744 | 2026-08-03 09:32:46 | 26 | ||||||
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Expression Patterns for C. elegans promoter GFP fusions Resource Report Resource Website 1+ mentions |
Expression Patterns for C. elegans promoter GFP fusions (RRID:SCR_001619) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of expression patterns of C. elegans promoter::GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. All of the strains in the expression pattern database are displayed in the browse page. The records are organized by gene; information such as locus name, genomic location (WormBase), the presence of images and videos, and the actual expression pattern are shown in a tabular format. | expression, gene, gene expression, caenorhabditis elegans, c. elegans, genomic, green fluorescent protein, location, locus, pattern, stage, strain, tissue |
is listed by: One Mind Biospecimen Bank Listing is related to: WormAtlas is related to: WormBase is related to: Caenorhabditis Genetics Center is related to: NEXTDB has parent organization: Albert Einstein College of Medicine; New York; USA |
Genome Canada ; Genome British Columbia |
PMID:17850180 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153885, nif-0000-25220, SCR_008354 | SCR_001619 | Caenorhabditis elegans Expression Patterns | 2026-08-03 09:31:29 | 4 | ||||||
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BodyMap-Xs Resource Report Resource Website 1+ mentions |
BodyMap-Xs (RRID:SCR_001147) | BodyMap-Xs | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008 | expressed sequence tag, comparative genomics, anatomy, taxonomy, brain, blood, connective, reproductive, muscular, alimentary, lung, liver, urinary, endocrine, exocrine, embryo, homology, gene expression, ortholog, paralog | has parent organization: DNA DataBank of Japan (DDBJ) | Neoplasm, Normal | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; New Energy and Industrial Technology Development Organization |
PMID:16381946 PMID:11125076 PMID:10592203 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02617 | http://bodymap.jp/, http://bodymap.ims.u-tokyo.ac.jp/ | SCR_001147 | BodyMap-Xs: anatomical and taxonomical breakdown of animal EST, BodyMap, BodyMap- human and mouse gene expression database, BodyMap: human and mouse gene expression database, BodyMap-cross species, BodyMap-Xs(cross species) | 2026-08-03 09:31:16 | 1 | |||
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cisRED: cis-regulatory element Resource Report Resource Website 10+ mentions |
cisRED: cis-regulatory element (RRID:SCR_002098) | cisRED | data or information resource, database | Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species. | atomic motif, conserved sequence motif, motif pattern, regulatory element, motif, atomic, promoter, chip-seq, transcription factor binding site, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: BC Cancer Agency |
Genome Canada ; BC Cancer Foundation ; Michael Smith Foundation for Health Research |
PMID:16381958 | Free, Freely available | nif-0000-02665, biotools:cisred, OMICS_01857, r3d100010619 | https://bio.tools/cisred, https://doi.org/10.17616/R3XK69 | SCR_002098 | cisRED - Databases of genome-wide regulatory module and element predictions | 2026-08-03 09:31:44 | 14 | ||||
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Spliceosome Database Resource Report Resource Website 10+ mentions |
Spliceosome Database (RRID:SCR_002097) | Spliceosome Database | data or information resource, database | A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes. | splicing, mass spectrometry, protein, rna, complex, spliceosome, small nuclear rna, structure, dynamics, ortholog, gene |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:23118483 | Free, Freely available | OMICS_01891 | SCR_002097 | Spliceosome Database - A source of information for the SLPICEOSOME: The large ribonucleoprotein complex responsible for pre-mRNA splicing, Spliceosome Component Database | 2026-08-03 09:31:33 | 11 | ||||||
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GermOnline Resource Report Resource Website 10+ mentions |
GermOnline (RRID:SCR_002807) | GermOnline | data or information resource, database | Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repository, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: OMA Browser has parent organization: National Institute of Health and Medical Research; Rennes; France |
Swiss Institute of Bioinformatics ; bioinformatics platform of Biogenouest ; National Institute of Health and Medical Research; Rennes; France ; University of Rennes 1; Rennes; France |
PMID:21149299 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:germonline, nif-0000-02906, r3d100010248 | https://bio.tools/germonline, https://doi.org/10.17616/R37K5Q | SCR_002807 | 2026-08-03 09:32:09 | 17 | |||||
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Unified Human Interactome Resource Report Resource Website 10+ mentions |
Unified Human Interactome (RRID:SCR_005805) | UniHI | data or information resource, database | 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 | 2026-08-03 09:32:47 | 19 | ||||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | data analysis service, service resource, analysis service resource, production 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 | 2026-08-03 09:32:56 | 36 | |||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | data analysis service, service resource, analysis service resource, production service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-08-03 09:32:59 | 3 | ||||||
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DroID - Drosophila Interactions Database Resource Report Resource Website 10+ mentions |
DroID - Drosophila Interactions Database (RRID:SCR_006634) | DroID | data or information resource, database | A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available. | interaction, gene, protein, protein interaction, annotation, transcription factor, rna, protein-protein interaction, interactome, gene expression, phenotype, interolog, ortholog |
is listed by: OMICtools is related to: Cytoscape has parent organization: Wayne State University School of Medicine; Michigan; USA |
PMID:21036869 PMID:18840285 |
Free, Public, Acknowledgement requested | nif-0000-02767, OMICS_01908 | SCR_006634 | DroID - The Drosophila Interactions Database | 2026-08-03 09:33:08 | 35 | ||||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | data analysis service, service resource, analysis service resource, production service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-08-03 09:33:21 | 0 |
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If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
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