2007 (English)In: The Ethics and Governance of Human Genetic Databases: European Perspectives / [ed] Matti Häyry, Ruth Chadwick, Vilhjálmur Árnason & Gardar Árnason, Cambridge: Cambridge University Press, 2007, no 4, 108-119 p.Chapter in book (Other academic) ...
770 full-length cDNAs. Analysis of the mouse transcriptome based on functional annotation of 60s profile, publications, research topics, and co-authors
The Gene Expression Database (GXD) is a community resource that stores and integrates expression information for the laboratory mouse, with a particular emphasis on mouse development, and makes these data freely available in formats appropriate for comprehensive analysis. GXD is implemented as a relational database and integrated with the Mouse Genome Database (MGD) to enable global analysis of genotype, expression and phenotype information. Interconnections with sequence databases and with databases from other species further extend GXDs utility for the analysis of gene expression data. GXD is available through the Mouse Genome Informatics Web Site at http://www.informatics.jax.org/
In a continuation of a 2014 conference that explored regulatory considerations and strategies for next-generation sequencing, the Friends of Cancer Research, with support from Alexandria Real Estate Equities, Inc, Pasadena, California, met to discuss the issues and problems of coordinating drug and diagnostic development, specifically the use of curated databases.. Ellen V. Sigal, PhD, Chair and Founder of Friends of Cancer Research, introduced the gathering by noting that high-throughput genomic technologies, including next-generation sequencing, allow for rapid assessment of many analytes and can help predict patients risk of developing certain cancers and how they might respond to therapies. "There are many advantages of high-throughput sequencing over that of a single analyte, but demonstrating its adequacy for clinical use is challenging, particularly the tension between the need to ensure validity and the practical limitations of submitting data for every possible variant.". She added ...
TY - JOUR. T1 - Analysis of the mouse transcriptome for genes involved in the function of the nervous system. AU - Gustincich, Stefano. AU - Batalov, Serge. AU - Beisel, Kirk W.. AU - Bono, Hidemasa. AU - Carninci, Piero. AU - Fletcher, Colin F.. AU - Grimmond, Sean. AU - Hirokawa, Nobutaka. AU - Jarvis, Erich D.. AU - Jegla, Tim. AU - Kawasawa, Yuka. AU - LeMieux, Julianna. AU - Miki, Harukata. AU - Raviola, Elio. AU - Teasdale, Rohan D.. AU - Tominaga, Naoko. AU - Yagi, Ken. AU - Zimmer, Andreas. AU - Arakawa, Takahiro. AU - Waki, Kazunori. AU - Kawai, Jun. AU - Hayashizaki, Yoshihide. AU - Okazaki, Yasushi. PY - 2003/6/1. Y1 - 2003/6/1. N2 - We analyzed the mouse Representative Transcript and Protein Set for molecules involved in brain function. We found full-length cDNAs of many known brain genes and discovered new members of known brain gene families, including Family 3 G-protein coupled receptors, voltage-gated channels, and connexins. We also identified previously unknown candidates for ...
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent ...
The "browser" lines at the beginning of the custom track indicate which native tracks to turn on along their visibilities, while the "hide all" line turns all the other native tracks off. In addition to these basic instructions there are many more examples on the UCSC Genome Browser Wiki.. What about when you want to view a genome and annotations not hosted on our site? If you have a FASTA file of your genome available, you can use faToTwoBit to convert your genome into a 2bit file, then make an assembly hub out of your data. Once youve created your hub, you can view the hub with the hubUrl setting. As an example, I have hosted an assembly hub for Arabadopsis thaliana here, and I can view the hub via a single URL like so ...
The GMOD project is a confederation of intercompatible open-source projects developing software tools for storing, managing, curating, and publishing biological data. Although the GMOD project originated from the goal of developing a generic tool set for common needs among model organism databases, GMOD tools are meanwhile used by many large and small, collaborative and single-investigator biological database projects for the dissemination of results of experimental research and curated knowledge. GMODs software tools provide a powerful and feature-rich basis for working with biological, in particular genomic and other molecular data. However, due to GMODs historical emphasis on single-genome projects many GMOD tools still lack features that are critical to effectively support the comparative, phylogenetic, and natural diversity-oriented questions frequently asked in evolutionary research. Recent developments have given rise to a window of opportunity for forging collaborations towards filling ...
Researchers from the University of Maryland School of Medicines (UMSOM) Institute for Genome Sciences (IGS) have created VIRGO (human vaginal non-redundant gene catalog): the first genomic catalog of the vaginal microbiome.
To whom it may concern: The completion of the sequencing of the entire DNA of the S. cerevisae genome, is a major event in the history of biology. All those involved are to be congratulated as we now have the first full genetic blueprint of a free living eukaryotic organism. The analysis of these gene products will provide us with a powerful tool for reading the genomes of other eukaryotes, particularly those of higher eukaryotes, which represent the majority of the data currently in the genetic databases. The analysis of the yeast genome is provided a useful framework for the annotation of many of the complete genome projects currently nearing completion, as well as the upcoming human genome. The yeast sequence information used to create this yeast webpage was provided by the GeneQuiz Consortium and the Mips Genome Commission . We have made an initial attempt to integrate these two data structures as well as supplement their annotation with that obtained ,From a set of functionally diagnostic ...
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SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree ...
Notice to our users== Please help us to improve this small molecules wiki and our other wikis by registering for a wiki account through our normal feedback email. ==Important small molecule references== *[http://www.xenbase.org/literature/article.do?method=display&articleId=35021 Database of Small Molecules by Feldman and Hogue 2006] at [https://pubchem.ncbi.nlm.nih.gov/ PubChem] *[http://www.xenbase.org/literature/article.do?method=display&articleId=47903 Wnt/Notch by Myers and Krieg 2014] *[http://www.xenbase.org/literature/article.do?method=display&articleId=970 Ubiquitin-proteasome by Salic and King 2005] ==Alphabetical List of Small Molecules With Literature References== *[[1,3-Dicyclohexylurea]] *[[11-cis retinal]] *[[18alpha-glycyrretinic acid]] *[[2-deoxyadenosine]] *[[2-APB]] *[[2-Deoxyglucose]] *[[3,3,5-triiodothyronine (T3)]] *[[5HT (seratonin)]] *[[8-Pcpt-2-O-Me-cAMP-AM]] *[[activin]] *[[Adenosine, periodate oxidized]] *[[AG1296]] *[[AG1879]] *[[AGN193109]] *[[alpha-amanitin]] ...
An integrated database resource consisting of 16 main databases, which are categorized into systems, genomic, chemical and health information. The PATHWAY, BRITE and MODULE databases in the systems information category contain KEGG pathway maps, BRITE hierarchy and table files and KEGG modules, respectively, as representations of high-level functions. They are all manually created based on published literature. The genomic information category contains the GENOME and GENES databases for collections of organisms with complete genomes and their gene catalogs, which are mostly taken from RefSeq and GenBank databases. The COMPOUND, GLYCAN, REACTION, RPAIR, RCLASS and ENZYME databases in the chemical information category contain chemical substances and reactions and are collectively called KEGG LIGAND for historical reasons. The health information category consists of the DISEASE, DRUG, DGROUP and ENVIRON databases for disease and drug information.
The list of gene annotated to the pathway term are provided by species, in a tabular form that can be sorted by several criteria (thin arrow). The default is the set of rat genes with choices for the mouse and human genes (thick arrow). The table provides links to the GBrowse tool for the rat and human genes [for more on GBrowse see the help page available here] and the references used in the annotation process along with information on the chromosome, start and stop positions. The A icon at the far right end of an entry, stands for Annotations and provides a link to a page with all the annotations for that gene across all ontologies RGD is using. Note that one can select to see annotations to the term and the terms descendants or only to the term by selecting or deselecting the box show annotations for terms descendants, respectively (thin arrow). Clicking on the icon tree to the right of the pathways name (circled), here interleukin-1 signaling pathway brings up the tree view of the ...
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Web Portal for International Cancer Research: Cancer Epidemiology and Genetic Databases, Research Programmes, Electronic Publications, Scientific Papers, IARC Press Releases, IARC Training Courses, IARC Fellowships for Cancer Research, IARC Meetings, etc
Strain reports include a comprehensive description of function and biological process as well as disease, expression, regulation and phenotype information.
Table 1. Expression of chondroadherin in mouse ocular tissues. Summary of expression analyses for chondroadherin in mouse ocular tissues based upon RT-PCR, in situ hybridization, and immunohistochemistry. The minus sign indicates no expression by immunochistochemistry; the ± sign indicates low expression by immunohistochemistry; the single plus sign indicates moderate expression by immunochistochemistry; and the triple plus sign indicates high expression by immunohistochemsitry. The cornea, lens, and retina were all positive by PCR and by in situ hybridization, while the retina was also positive by the following entries from the Gene Expression Omnibus (GEO) profiles (Entry: GDS592,GPL1073, Experiment: Large scale analysis of the mouse transcriptiome; Entry: GDS182,GPL81, Experiment: Large scale analysis of the mouse transcriptome).. ...
TL;DR: NIH are scaling back funding on model organism databases, which will degrade annotation quality. This can have far-reaching implications in many aspects of biology and computational biology. Theres a letter you can sign electronically, please do. ,http://www.genetics-gsa.org/MODsupport, I am hoping to write a more detailed post on why this is important, but for the […]. ...
If using the UCSC Genes track, consider showing only one transcript per gene by turning off splice variants on the track configuration page ...
On the web site the seem to define this project as an attempt to "collect variation causing disease (mutations) in all genes world wide" so I guess that is what variome means to them. So - I wonder here - what is wrong with "polymorphisms ...
InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response ...
Search for terms in track descriptions, groups, and names. If multiple terms are entered, only tracks with all terms will be part of the results ...
Search for terms in track descriptions, groups, and names. If multiple terms are entered, only tracks with all terms will be part of the results ...
What can I find? DNA methylation, transcription factor binding sites, histone modifications, and regulatory features such as enhancers and repressors, and microarray annotations.. ...
Property "Dpi dataset" (as page type) with input value "{{{DPIdataset}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "TSS like by RIKEN classifier" (as page type) with input value "{{{TSSclassifier}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "DHS support" (as page type) with input value "{{{DHSsupport}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. ...
Property "Dpi dataset" (as page type) with input value "{{{DPIdataset}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "TSS like by RIKEN classifier" (as page type) with input value "{{{TSSclassifier}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "DHS support" (as page type) with input value "{{{DHSsupport}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. ...
Datasets are collections of data. BioGPS has thousands of datasets available for browsing and which can be easily viewed in our interactive data chart. Learn more.. ...
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chr1:182842526-183063694, + strand. Annotation of mouse strain SPRET/EiJ genome assembly provided by the University of California Santa Cruz (UCSC) Genome Browser Group and the Wellcome Sanger Institutes Mouse Genomes Project (MGP). Distributed via Ensembl Release 92. Gene type: protein coding gene; Gene Name: Cdc42bpa ...
chr2:58705780-58831955, - strand. Annotation of mouse strain CAROLI/EiJ genome assembly provided by the University of California Santa Cruz (UCSC) Genome Browser Group and the Wellcome Sanger Institutes Mouse Genomes Project (MGP). Distributed via Ensembl Release 92. Gene type: protein coding gene; Gene Name: Fign ...
A list of Go definitions, with pointers to parent nodes. Read from the .obo file. The user may construct the explicit hierachy by storing these in a Map or similar ...
Datasets are collections of data. BioGPS has thousands of datasets available for browsing and which can be easily viewed in our interactive data chart. Learn more.. ...
p,Transcripts predicted by comparative Augustus with RNA-seq information. Predicted with a coding model, but not guaranteed to have a ORF with homology to known proteins.,/p,Unknown likely coding ...
Search the selected model organism database for genes or proteins by a variety of criteria, including name, sequence size or location, evidence code, GO term, publication, etc.
We found that human genome coding regions annotated by computers have different kinds of many errors in public domain through homologous BLAST of our cloned genes in non-redundant (nr) database, including insertions, deletions or mutations of one base pair or a segment in sequences at the cDNA level …
This detailed view shows all details of the selected patient, including all variants reported in this patient. At the bottom of the page, all variants reported in this patient are listed, with the one you are looking at in bold. The link to the UCSC Genome Browser will show the browser zoomed in to the location of the selected variant ...
We have used all reasonable efforts to ensure that the information displayed on these pages and contained in the databases is of high quality. We make no warranty, express or implied, as to its accuracy or that the information is fit for a particular purpose, and will not be held responsible for any consequences arising out of any inaccuracies or omissions. Individuals, organisations and companies which use this database do so on the understanding that no liability whatsoever either direct or indirect shall rest upon the curator(s) or any of their employees or agents for the effects of any product, process or method that may be produced or adopted by any part, notwithstanding that the formulation of such product, process or method may be based upon information here provided ...
We have used all reasonable efforts to ensure that the information displayed on these pages and contained in the databases is of high quality. We make no warranty, express or implied, as to its accuracy or that the information is fit for a particular purpose, and will not be held responsible for any consequences arising out of any inaccuracies or omissions. Individuals, organisations and companies which use this database do so on the understanding that no liability whatsoever either direct or indirect shall rest upon the curator(s) or any of their employees or agents for the effects of any product, process or method that may be produced or adopted by any part, notwithstanding that the formulation of such product, process or method may be based upon information here provided ...
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 Dec; 17(12):1797-808. PMID: 17984227; PMCID: PMC2099589. ...
Complete information for COL16A1 gene (Protein Coding), Collagen Type XVI Alpha 1 Chain, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Zhou J (2008) CST Curation Set: 5472; Year: 2008; Biosample/Treatment: cell line, Jurkat/untreated; Disease: T cell leukemia; SILAC: -; Specificities of Antibodies Used to Purify Peptides prior to LCMS: (K/R)XpSX(K/R)Antibodies Used to Purify Peptides prior to LCMS: Phospho-(Ser) PKC Substrate Antibody Cat#: 2261, PTMScan(R) Phospho-PKC Substrate Motif (K/RXpSXK/R) Immunoaffinity Beads Cat#: 1985 ...
Zhou J (2008) CST Curation Set: 5314; Year: 2008; Biosample/Treatment: cell line, Jurkat/TPA; Disease: T cell leukemia; SILAC: -; Specificities of Antibodies Used to Purify Peptides prior to LCMS: (K/R)XpSX(K/R)Antibodies Used to Purify Peptides prior to LCMS: Phospho-(Ser) PKC Substrate Antibody Cat#: 2261, PTMScan(R) Phospho-PKC Substrate Motif (K/RXpSXK/R) Immunoaffinity Beads Cat#: 1985 ...
Since 1984, MMP, Inc. brings a concept of highly individualized assistance and service, striving to provide our clientele with unique resources. At MMP our mission is to manufacture raw materials of the highest quality for cosmetic and personal care applications with customized service. Our team is continuously working on the development of... Learn more » ...
Combining tracking of SAR units, personnel, vessels, missions, training, equipment, and administrative data across the region in a single web accessible database with dynamic links to other data sources (RCC) and endless potential for growth.
We have siRNA for most human, mouse and rat genes. To find siRNA for your gene, first search for your gene (using a gene name, gene ID or gene accession number) using the search tool bar, and then click on the ��siRNA�� hyperlink on the right hand side of your intended gene description in the ��Genes�� results field ...
The NCBI GEO and ArrayExpress databases were extensively searched for environmental conditions leading to apoptosis in 293T cells and genes differentially expressed under these conditions. The following data was obtained: ...
v1.2.014963.t1(symbB.v1.2.014963.t1) v1.2.023547.t1(symbB.v1.2.023547.t1) v1.2.027690.t1(symbB.v1.2.027690.t1) v1.2.027690.t2(symbB.v1.2.027690.t2) v1.2.027690.t3(symbB.v1.2.027690.t3) v1.2.032089.t1(symbB.v1.2.032089.t1) v1.2.032880.t1(symbB.v1.2.032880.t1 ...
v1.2.007921.t2(symbB.v1.2.007921.t2) v1.2.007922.t1(symbB.v1.2.007922.t1) v1.2.007922.t2(symbB.v1.2.007922.t2) v1.2.007922.t3(symbB.v1.2.007922.t3) v1.2.016339.t1(symbB.v1.2.016339.t1 ...
de Leeuw N, Dijkhuizen T, Hehir-Kwa JY, Carter NP, Feuk L, Firth HV, Kuhn RM, Ledbetter DH, Martin CL, van Ravenswaaij-Arts CM, Scherer SW, Shams S, Van Vooren S, Sijmons R, Swertz M, Hastings R. Diagnostic interpretation of array data using public databases and internet sources. Hum Mutat. 2012 Jun;33(6):930-40. PMID: 26285306; PMC: PMC5027376 Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23. PMID: 22086951; PMC: PMC3245018. ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, BLAST homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. ...
The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGDs primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and
A program written by UCSC student Jim Kent, called GigAssembler, is used to periodically assemble a widely used public draft version of the human genome sequence using updated data from GenBank at the National Center For Biotechnology Information (NCBI). This assembly is steadily improving as the the public sequencing consortium churns out new data. We will look at the coverage statistics on the latest assembly, and then look at web tools to explore it, and what they find. The three most widely used public annotation browsers are the UCSC Genome browser (genome.ucsc.edu), the Ensembl genome browser (www.ensembl.org), and the NCBI map viewer (www.ncbi.nlm.nih.gov/genome/guide), the latter based on NCBIs own sequence assembly. We will focus on the UCSC browser, which shows a rich variety of data mapped to the genome sequence, including predicted genes, expressed sequence tags, full length mRNAs, genetic and radiation hybrid map markers, cytogenetically mapped clones, single nucleotide ...
2.40 - 3.00 Noelle Cockett: Assembly of the Ovine Whole Genome Reference Sequence. 3.00 - 3.30 coffee/tea. 3.30 - 3.50 Lisa Stubbs: Rapidly evolving transcription factor genes: the KRAB-family (video-conference). 3.50 - 6.00 Discussion on nomenclature guidelines across species - chair Alan Archibald. 7:00dinner. Day 2 (13th October):. Start 9.00 - coffee/tea. Gene Family Nomenclature - chair Vasilis Vasiliou ...
Don Gilbert pointed out that cheap short sequencers are now available. Lots of people have inexpensive sequnces, but there still is no way to do cheap annotation. Current GMOD clients are species or family centered. Want to make it easy to integrate multiple species. ApiDB is at the point of opening new species databases and web sites with relatively little effort. Comparative genomics came up over and over again, both across species and within species. As data grows and is consolidated, issues of who owns the data and whos responsible for the annotation become more problematic. How does GMOD want to deal with integration issues? How close to the sequencer does GMOD want to get? We dont want to pull the data off the sequencer. Should we position GMOD as something that can feed data into places like Ensembl? Ensembl does not have curation expertise of the MODs. Even if NCBI is wonderful at consolidation, they wont have quality curation. GMOD sits right there, supporting curation. So, we doubt ...
RiceGE : Rice Functional Genomics Database. gebd Rice Genome Browser. iSect Tools, iView Tools and Gene Expression Atlas. Collection of Rice T-DNA/Ds, Rice cDNA, Marker, EST, MPSS, SAGE, Arabidopsis, Maize, Wheat, Barley Homology, Rice Tiling Array and Gene Expression Data. Created and developed by Huaming Chen
RiceGE : Rice Functional Genomics Database. gebd Rice Genome Browser. iSect Tools, iView Tools and Gene Expression Atlas. Collection of Rice T-DNA/Ds, Rice cDNA, Marker, EST, MPSS, SAGE, Arabidopsis, Maize, Wheat, Barley Homology, Rice Tiling Array and Gene Expression Data. Created and developed by Huaming Chen
Dear Pegah Tavakolkhah, , I have one more question. I have read in the description of some GOs , that they are involved in apoptosis or angiogenesis (which are the main , reasons of cancer). I wanted to know if apoptosis or angiogenesis are GO , themselves. And if they are, would their descendant GOs show the GOs , which are responsible for these two processes? If you do a search for terms either using GOOSE or using AmiGO (http://amigo.geneontology.org/), you can find the GO terms apoptosis (GO:0006915; http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0006915) and angiogenesis (GO:0001525; http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0001525). You can find the gene products that have been associated with these processes (and the more specific child processes), either by choosing the gene product associations link in AmiGO, or by using GOOSE to query the GO database. I hope that is helpful; if you have any more questions, please dont hesitate to ...
GO annotations: Mouse from MGI; Human from GO Annotations @ EBI (GOA); Rat from RGD; Chicken from GOA; Fly from FlyBase; Pfalc from PlasmoDB; Worm from WormBase; Dicty from dictyBase; Yeast from SGD; Zfin from ZFIN; Tair from TAIR/TIGR; Rice from Gramene; Pombe from Sanger GeneDB ...
Representation and depiction of phenotype information at SOC and HLT level. (A) We used the hierarchical information of the MedDRA ontology to map all phenotypi
FatiGO is a web-accessible application that functions in much the same way as DAVIDs GoCharts, including the ability to specify term-specificity level. Unlike DAVID, FatiGO does not allow the setting of a minimum hit threshold for simplified viewing of only the most highly represented functional categories. Likewise, FatiGO limits the graphical output to only one top-level GO category at a time, whereas DAVID allows the combined viewing of biological process, molecular function, and cellular component annotations simultaneously. FatiGOs static barchart output looks very similar to DAVIDs GoChart; an important distinction is that DAVIDs GoCharts are dynamic, allowing users to drill-down and traverse the GO hierarchy for any subset of genes, view the underlying chart data and associated annotations, and link out to external data repositories including LocusLink and QuickGO. As shown in Table 3 the majority of accession types accepted and functional annotations offered by DAVID are not ...
Description: This session displays a region of the LHX6 gene that highlights a selection of the new tracks added in the previous year for the hg38/GRCh38 human assembly. The tracks shown in this display (from top to bottom) include GENCODE Genes V22, transcription levels assayed across 9 ENCODE cell lines, DNase hypersensitive regions based on data from 95 ENCODE cell lines, genome-wide conservation scores calculated using phastCons, a multiple genome alignment created using Lastz and Multiz, and pathogenic CNVs from the ClinGen database. Adapted from Figure 1 in Speir, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 2016 Jan 4;44(D1):D717-25: http://nar.oxfordjournals.org/content/44/D1/D717. ...
Description: This session displays a region of the LHX6 gene that highlights a selection of the new tracks added in the previous year for the hg38/GRCh38 human assembly. The tracks shown in this display (from top to bottom) include GENCODE Genes V22, transcription levels assayed across 9 ENCODE cell lines, DNase hypersensitive regions based on data from 95 ENCODE cell lines, genome-wide conservation scores calculated using phastCons, a multiple genome alignment created using Lastz and Multiz, and pathogenic CNVs from the ClinGen database. Adapted from Figure 1 in Speir, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 2016 Jan 4;44(D1):D717-25: http://nar.oxfordjournals.org/content/44/D1/D717. ...
Symbol: This is the official symbol assigned to this strain according to the strain nomenclature guidelines. This is a combination of strain and substrain designations for inbred strains (or symbol and ILAR code for other strain types).. Strain: The official strain symbol.. Substrain: The official substrain symbol - this can be a collection of ILAR lab codes defining the history of this particular strain. Can also be found in pulldown section below with links to the strain report pages.. Full Name: If the strain has a text name then it is displayed here; this is not visible if no name is associated to the strain, as in this example. Ontology ID: The identification number of the strain ontology term assigned by RGD, linked to the term in the ontology browser. In the strain ontology, rat strains are organized in a hierarchical fashion based on the type of strain and the way they were developed.. Also known as: Old symbols and synonyms that were used for the strain. If a strain is renamed to comply ...
Notice This is our old gene family archive which is no longer maintained. Please visit our new gene family pages for up to date family data.
Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.. Ensembl receives major funding from the Wellcome Trust. Our acknowledgements page includes a list of additional current and previous funding bodies.. ...
Prior to requesting the BIOLOGICAL RESOURCE, the RECIPIENT must obtain approval from the DEPOSITOR using the Approval Form. In publishing the research results obtained by use of the BIOLOGICAL RESOURCE, a citation of the following literature(s) designated by the DEPOSITOR is requested. Mol. Cell Neurosci., 34, 261-270 (2007).In publishing the research results to be obtained by use of the BIOLOGICAL RESOURCE, an acknowledgment to the DEPOSITOR is requested. The availability of the BIOLOGICAL RESOURCE is limited to a RECIPIENT of a not-for profit institution for a not-for-profit research. For use of the BIOLOGICAL RESOURCE by a for-profit institution, the RECIPIENT must reach agreement on terms and conditions of use of it with DEPOSITOR and must obtain a prior written consent from the DEPOSITOR. RECIPIENT must contact the DEPOSITOR in the case of application for any patents or commercial use based on the results from use of the BIOLOGICAL RESOURCE ...
Click on a feature for details. Click or drag in the base position track to zoom in. Click side bars for track options. Drag side bars or labels up or down to reorder tracks. Drag tracks left or right to new position ...
and COPS2 gene details page in the UCSC Genome Browser. Human CSN2 genome location and CSN2 gene details page in the UCSC Genome Browser. Wolf DA, ...
Click on a feature for details. Click or drag in the base position track to zoom in. Click side bars for track options. Drag side bars or labels up or down to reorder tracks. Drag tracks left or right to new position. Press "?" for keyboard shortcuts ...
Click on a feature for details. Click or drag in the base position track to zoom in. Click side bars for track options. Drag side bars or labels up or down to reorder tracks. Drag tracks left or right to new position. Press "?" for keyboard shortcuts ...
Click on a feature for details. Click or drag in the base position track to zoom in. Click side bars for track options. Drag side bars or labels up or down to reorder tracks. Drag tracks left or right to new position. Press "?" for keyboard shortcuts ...
Genome databases for Trichomonas vaginalis. Genomic-scale data available via TrichDB may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries can also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities of cells and organisms from both high‐level and genomic perspectives
Views in Archive EnsEMBL are separated into gene based views and transcript based views according to which level the information is more appropriately associated with. This view is a transcript level view. To flip between the two sets of views you can click on the Gene and Transcript tabs in the menu bar at the top of the page. ...
Views in Archive EnsEMBL are separated into gene based views and transcript based views according to which level the information is more appropriately associated with. This view is a transcript level view. To flip between the two sets of views you can click on the Gene and Transcript tabs in the menu bar at the top of the page. ...
KEGG organisms are assigned 3 letter codes, e.g., hsa for homo sapiens. To map these codes to the NCBI taxonomy ID, a one-liner sed command is sufficient: First download by copy n paste from the KEGG taxonomy page: Save it to a text file kegg_taxonomy.txt Then sed: Download kegg2taxonomy.txt
Upload a list of gene IDs You can upload any file that has a whitespace (returns, tabs, or spaces) separated list of gene IDs. Be sure to view the results of our gene ID mapping to ensure your list was mapped correctly. ...
Upload a list of gene IDs You can upload any file that has a whitespace (returns, tabs, or spaces) separated list of gene IDs. Be sure to view the results of our gene ID mapping to ensure your list was mapped correctly. ...
The data in Mouse Polymorphism DB has been moved to NIG Mouse Genome Database. With this, we are stopping all our services except the Blast search. Thank you for using the Mouse Polymorphism DB till now. We hope that you will continue to support the NIG Mouse Genome Database ...
Today, a novel map of all proteins secreted to human blood is described. The paper by Uhlen et al. entitled "The Human Secretome" is published in the journal Science Signaling and provides a first comprehensive annotation of all proteins secreted by the human cells. In addition, an analysis of the concentrations of the proteins circulating in the human blood is described. This map provides a unique resource to study human biology and diseases, in particular for immune-based research and efforts to develop new, effective treatments in oncology and autoimmune diseases...Read more. ...
Today, a novel map of all proteins secreted to human blood is described. The paper by Uhlen et al. entitled "The Human Secretome" is published in the journal Science Signaling and provides a first comprehensive annotation of all proteins secreted by the human cells. In addition, an analysis of the concentrations of the proteins circulating in the human blood is described. This map provides a unique resource to study human biology and diseases, in particular for immune-based research and efforts to develop new, effective treatments in oncology and autoimmune diseases...Read more. ...
Related human diseases are listed by referencing the following databases: KEGG disease (http://www.genome.jp/kegg/disease/), GeneCards (http://www.genecards.org/), and Online Mendelian Inheritance in Man (http://www.ncbi.nlm.nih.gov/omim ...
The IP Industry Base is a public available database about the global market of IP practitioners. Currently is provides high-quality profiles of more than 4910 companies, 15620 professionals and 4250 places. The service of the IP Industry Base is dedicated to technology managers, IP professionals and IPR academia. The open data of the IP Industry Base aims to create transparency for the market of IP practitioners.
The IP Industry Base is a public available database about the global market of IP practitioners. Currently is provides high-quality profiles of more than 4890 companies, 16130 professionals and 4290 places. The service of the IP Industry Base is dedicated to technology managers, IP professionals and IPR academia. The open data of the IP Industry Base aims to create transparency for the market of IP practitioners.
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KEGG pathway frequency heatmap. All coding genes annotated against KEGG database and KEGG pathway frequencies were hierarchically clustered in two dimensions. T
Today is National Eggnog Day. Celebrate this tasty beverage and get your eggnog fix this holiday with one of these mouthwatering recipes.
The following is an overview of the steps required to submit an application for the SCAP-T data:. 1. All applications need to be submitted to dbGaP through the dbGaP Authorized Access web page. For instructions on how to request dbGaP data please view the dbGaP Request Procedures (PDF). Please log in using your eRA Commons account (NIH intramural investigators should use their NIH login) and enter your application.. 2. The dbGaP dataset ID for SCAP-T is phs000833.v3.p1. Click here to go to our project website on dbGaP.. © 2015 University of Pennsylvania ...