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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System Resource Report Resource Website 1+ mentions |
MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System (RRID:SCR_007661) | atlas, data or information resource, data processing software, software application, software resource, training resource | An interactive database of the Drosophila melanogaster nervous system. It is used by the drosophila neuroscience community and by other researchers studying arthropod brain structure. Flybrain contains neuroanatomical peer reviewed descriptions of the central and peripheral nervous system of Drosophila melanogaster. It also contains an introductory hypertext tour guide to the basic structure of the nervous system, as well as more specific information concerning different anatomical structures, developmental stages, and visualization techniques for the Drosophila nervous system. Additionally, The site contains schematic representations, a 3D project, immunocytology stains, a library of golgi impregnations, and enhancer-trap images. | drosophila melanogaster, drosophila melanogaster nervous system, drosophila melanogaster neuroanatomy, ganglion, gene, 3-dimensional, abdominal, anatomy, arthropod, autofluorescence, chemical, development, developmental, golgi, histology, immunocytology, impregnation, map, model, morphology, nervous system, neuroanatomical, neuroanatomy, neuron, neuropil, periphery, phenotype, structure, thoracic, visualization |
has parent organization: National Institute for Basic Biology; Okazaki; Japan has parent organization: University of Arizona; Arizona; USA has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
nif-0000-02843 | SCR_007661 | FlyBrain | 2026-09-19 12:51:32 | 5 | |||||||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | d spatial image, data or information resource, data repository, database, image collection, service resource, storage service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-09-19 12:51:32 | 7 | |||||
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Connectome Mapping Toolkit Resource Report Resource Website 10+ mentions |
Connectome Mapping Toolkit (RRID:SCR_001644) | Connectome Mapping Toolkit | data management software, data or information resource, data processing software, data set, image analysis software, image processing software, software application, software resource, software toolkit | A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application. | magnetic resonance, connectome, mapping, data management, data sharing, visualization, analysis, connectome mapper, processing pipeline, python, connectomics, multi-modal, network analysis, neuroimaging, neuroinformatics tool, mri, knowledge-base, semantic, technology, mapping, source code |
is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: University of Lausanne; Lausanne; Switzerland has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland is parent organization of: Connectome Viewer |
Swiss National Science Foundation 33CM30-124089 | PMID:21713110 | Free, Available for download, Freely available | nlx_153920 | http://www.cmtk.org/, http://www.connectome.ch/ | SCR_001644 | 2026-09-19 12:49:44 | 10 | |||||
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APHIDBASE Resource Report Resource Website 50+ mentions |
APHIDBASE (RRID:SCR_001765) | AphidBase | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Aphid genome database. Facilitates community annotation of pea aphid genome by International Aphid Genomics Consortium (IAGC). It aims to store recently acquired genomic resources on aphids and compare them to other insect resources as functional annotation tools. AphidBase Information System designed to organize and distribute genomic data and annotations for large international community was constructed using open source software tools from Generic Model Organism Database (GMOD). | aphid, aphid gene sequence, aphid genome, aphid nervous system, genome, blast, annotate, annotation, est, function, FASEB list | has parent organization: INRA Rennes | ANR Exdisum ; ANR Genoplante ; Rennes Metropole |
PMID:20482635 PMID:17237053 |
Free, Freely available | nif-0000-02554 | http://w3.rennes.inra.fr/AphidBase | http://www.aphidbase.com/ | SCR_001765 | The Aphid Genome Database, Aphid Genome Database | 2026-09-19 12:49:48 | 69 | |||
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InteroPorc Resource Report Resource Website 1+ mentions |
InteroPorc (RRID:SCR_002067) | InteroPorc | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code | Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8. | orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Integr8 : Access to complete genomes and proteomes is related to: IntAct is related to: MINT is related to: Database of Interacting Proteins (DIP) is related to: PSICQUIC Registry has parent organization: CEA; Gif sur Yvette; France |
European Union FELICS 021902 RII3; Marie Curie Fellowship ; French National Agency of Research ANR Biosys06_134823 SULFIRHOM; French Atomic Energy Commission |
PMID:18508856 | Open unspecified license, Acknowledgement requested | nif-0000-20816, biotools:interoporc | https://bio.tools/interoporc | SCR_002067 | InteroPorc: Automatic molecular interaction predictions, Automatic molecular interaction predictions | 2026-09-19 12:49:52 | 6 | ||||
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modENCODE Resource Report Resource Website 100+ mentions |
modENCODE (RRID:SCR_006206) | modENCODE | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | 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 | 2026-09-19 12:51:06 | 260 | |||||
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microRNA.org Resource Report Resource Website 1000+ mentions |
microRNA.org (RRID:SCR_006997) | microRNA.org | data or information resource, database, software resource | Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microrna, gene, expression, gene regulation, FASEB list |
is listed by: OMICtools is listed by: SoftCite |
NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03127, OMICS_00402 | SCR_006997 | microRNA.org - Targets and Expression | 2026-09-19 12:51:22 | 2818 | |||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | data analysis software, data processing software, software application, software resource | 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) | 2026-09-19 12:51:46 | 8 | |||||
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dbVar Resource Report Resource Website 100+ mentions |
dbVar (RRID:SCR_003219) | dbVar | data or information resource, data repository, database, service resource, storage service resource | Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. | structure, variation, structural variation, genetics, insertion, deletion, copy number variant, inversion, translocation, genomic imbalance, genotype, gene expression, dna, genomics, phenotype, genetic code |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is related to: Database of Genomic Variants Archive (DGVa) is related to: Database of Genomic Variants has parent organization: NCBI |
PMID:23193291 | Free, Freely available | nlx_157217, r3d100010758 | https://doi.org/10.17616/R3V610 | SCR_003219 | dbVar, Database of Genomic Structural Variation, NCBI dbVar | 2026-09-19 12:50:19 | 198 | |||||
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PicTar Resource Report Resource Website 1000+ mentions |
PicTar (RRID:SCR_003343) | PicTar | software resource | An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets | microrna target, microrna, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
PMID:15806104 | Free, Available for download, Freely available | OMICS_00411, biotools:pictar, nif-0000-31983 | http://pictar.mdc-berlin.de/, https://bio.tools/pictar | SCR_003343 | 2026-09-19 12:50:17 | 1717 | ||||||
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BrainTrap: Fly Brain Protein Trap Database Resource Report Resource Website 1+ mentions |
BrainTrap: Fly Brain Protein Trap Database (RRID:SCR_003398) | BrainTrap | d spatial image, data or information resource, database | This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download. | brain, exon, expression, 3d confocal, affinity, antibody, dataset, immunohistochemical, microscopy, image, protein, protein-trap, gene | has parent organization: University of Edinburgh; Scotland; United Kingdom | EPSRC ; British society for Developmental Biology ; Society for Experimental Biology ; Virtual Fly Brain e-Science Institute Theme ; BBSRC ; MRC |
PMID:20624714 | Free, Freely available | nif-0000-32989 | http://fruitfly.inf.ed.ac.uk/braintrap/ | SCR_003398 | Fly Brain Protein Trap Database, Brain Trap | 2026-09-19 12:50:19 | 1 | ||||
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Cell Centered Database Resource Report Resource Website 10+ mentions |
Cell Centered Database (RRID:SCR_002168) | CCDB | data or information resource, data repository, database, image repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB. | electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomography |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: re3data.org is related to: Cell Image Library (CIL) is related to: Cell Image Library (CIL) is related to: Whole Brain Catalog is related to: Integrated Manually Extracted Annotation has parent organization: University of California at San Diego; California; USA has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR is parent organization of: Subcellular Anatomy Ontology is parent organization of: CCDB Image Converter is parent organization of: Jinx is parent organization of: WebImageBrowser is parent organization of: Image Workflow is parent organization of: Animal Imaging Database |
PMID:18054501 PMID:12160711 |
Free, Freely available | nif-0000-00007, r3d100000018 | SCR_002168 | CCDB, Cell-Centered Database | 2026-09-19 12:49:54 | 31 | ||||||
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MachiBase Resource Report Resource Website 1+ mentions |
MachiBase (RRID:SCR_003078) | MachiBase | data or information resource, database | Database for Drosophila melanogaster transcription profiling that allows users to search the Drosophilia genome, see sequence overviews, and look at various transcripts. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina / Solexa using a newly developed 5'-end mRNA collection method. Approximately 25 million 25-27 nucleotide (nt) 5'-end mRNA tags from the embryos, larvae, young males, young females, old males, old females, and S2 (culture cell line) of D. melanogaster were collected. By arranging this vast amount of expression tag with other annotated data, they have built a one-stop service for Drosophila melanogaster transcription profiling. | transcription profiling, genome, sequence, transcript, mrna, promoter, gene expression, development, embryo, larvae, young, male, female, old, s2, culture, cell line, expressed sequence tag, solexa |
is listed by: OMICtools has parent organization: University of Tokyo; Tokyo; Japan |
PMID:18842623 | Free, Available for download, Freely available | OMICS_01878, nif-0000-03092 | SCR_003078 | 2026-09-19 12:56:38 | 1 | |||||||
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MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation Resource Report Resource Website 10+ mentions |
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation (RRID:SCR_003077) | MAPPER, MAPPER 2, | data or information resource, database, service resource | A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs. | transcription factor binding site, gene promoter, intron, non-coding exon, transcription factor, chromosome, gene, homolog, rsnp, single nucleotide polymorphism, search engine |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA is parent organization of: rSNPs MAPPER |
PMID:15608292 PMID:15799782 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01877, nif-0000-03101 | http://bio.chip.org/mapper | SCR_003077 | Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER 2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER database | 2026-09-19 12:56:38 | 11 | |||||
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MapViewer Resource Report Resource Website 100+ mentions |
MapViewer (RRID:SCR_003092) | Map Viewer | data or information resource, database | 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 | 2026-09-19 12:56:38 | 244 | |||||||
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SignaLink Resource Report Resource Website 50+ mentions |
SignaLink (RRID:SCR_003569) | SignaLink | data or information resource, database | An integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. The multi-layered database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The website allows the interactive exploration of how each signaling protein is regulated. Features * experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; * combines manual curation with large-scale datasets; * provides confidence scores for each interaction; * operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML). | analyze, signaling, pathway, cross-talk, transcription factor, mirna, regulatory enzyme, protein, interaction, regulatory network, signaling pathway, scaffold protein, enzyme, signaling, drug discovery, regulatory, network, post-transcriptional regulator, transcriptional regulator, protein-protein interaction, post-translational modification, pathway regulator, FASEB list |
is related to: ConsensusPathDB has parent organization: Eotvos Lorand University; Budapest; Hungary |
PMID:23331499 PMID:20542890 |
Acknowledgement requested, Free for non-profit use | nlx_157704 | SCR_003569 | 2026-09-19 12:56:40 | 59 | |||||||
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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 | 2026-09-19 12:56:42 | 9 | |||||||
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Information Hyperlinked Over Proteins Resource Report Resource Website 10+ mentions |
Information Hyperlinked Over Proteins (RRID:SCR_004829) | iHOP | data or information resource, database, service resource | Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. | phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Autonomous University of Madrid; Madrid; Spain |
European Union IST-2001- 32688; European Union QLRT-2001-00015 |
PMID:15226743 | Creative Commons Attribution-NoDerivs License, Works v3 | biotools:ihop, nif-0000-00232, OMICS_01185 | https://bio.tools/ihop | SCR_004829 | iHOP - Information Hyperlinked over Proteins | 2026-09-19 12:56:47 | 24 | ||||
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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 | 2026-09-19 12:56:53 | 36 | |||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | analysis service resource, data analysis service, production service resource, 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 | 2026-09-19 12:56:57 | 3 |
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