We have integrated these data with the other types of expression data in gxd and with the genetic, functional, phenotypic and diseaserelated information in mgi and thus made them accessible to many new search capabilities. Is there a database to find out which genes are expressed. Recode the database of the translational recoding events. The data set consists of the expression levels of 77 proteinsprotein modifications that produced detectable signals in the nuclear fraction of cortex. Tools are provided to help users query and download experiments and curated gene expression profiles. Data and software availability gse89482 gse93179 gse93180 gse95587 friedman et al. The first step of the pipeline involves calculating the similarity between gene expression measured in a single cell with reference gene expression profiles from a public database, such as the fantom5 atlas functional annotation of mammalian genomes 5 arner et al. To request access to these releases, follow the instructions in oracle support document 1071023.
The server accepts a unique gene name gene alias or a gene signature name from the msigdb database there is an autocomplete mechanism to help finding the right names. Principal component analysis showed a strong clustering by tissue and a relatively good agreement between mouse and rat tissue specific sample clusters. A knowledgebased portal with genecentric expression profiles based on the annotation of several antibodies towards the same protein target. A bioconductor r package that lets you integrate your rnaseq or microarray data with your chipseq data. Expression array data analysis illumina expression beadchips are part of a complete gene expression solution that includes instrumentation, software, and reagent kits. Mendeley data gene expression profiles of mouse facial. The raw data has also been deposited to geo with the geo accession id gse29184. It corrects for gccontent bias and dna copy number aberrations. Clariom d and clariom s assays for human, mouse, and rat are designed for wholetranscriptome expression profiling and biomarker discovery. Rnaseq atlasa reference database for gene expression. Svm classifier to predict genes important for selfrenewal and pluripotency of mouse embryonic stem cells. These data are related to the research articles entitled spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences by feng et al, 2009 and systems biology of facial development. Mice protein expression data set uci machine learning. The brainspan project is a detailed atlas of gene expression across human development.
Bloodspot provides a plot of gene expression in hematopoietic cells at different maturation stages based on curated microarray data. These data files will enable investigators to obtain a rapid assessment of the relative expression level of any gene on the array with respect to time, tissue, prominence, and expression trajectory. Gene expression profile data for mouse facial development. In addition, we will assemble gene expression profiles for a few focused experiments that will test hypotheses related to the techniques employed, tumour models. There is one metacell for every subcluster, which contains the aggregate umi counts for all the singlecells that belong to that subcluster. Raw counts are provided for rnaseq datasets and normalized intensities are available for. A dataset for exploring the neuropathology and genomic features of disease and aging. It is very flexible as you can custom any entry on the preformed lists or you add your own. This database stores individual gene expression profiles from curated datasets in the gene expression omnibus geo repository. Because all the data on the human protein atlas are publicly available, the information can be integrated into other databases. Coexpedia is a database of contextassociated co expression networks inferred from individual series of microarray samples for human and mouse of geo. It lets you preprocess and create differential gene lists for both data sets.
Arrayexpress a public repository for microarray gene expression data at the ebi. Gxd collects and integrates the gene expression information in mgi. Thus, this atlas will include a data structure and data curation strategy that will facilitate the ongoing collection of gene expression data, even after the completion of this project. Its primary emphasis is on endogenous gene expression during mouse development. Both the srna expression profile of the mature mirna and the cage expression profile of its associated promoter can be visualized. The molecular signatures database msigdb is a collection of annotated gene sets for use with gsea software. Home expression team using the irap pipeline see above. Data can be downloaded and viewed in encode website.
Biogps mouse cell type and tissue gene expression profiles. View the expression profile of a gene set in a provided public expression compendia. Gxd has developed an rnaseq and microarray experiment search to quickly and reliably find specific mouse expression studies in arrayexpress and geo. Comparative data on inbred strain characteristics, snps, polymorphisms, and quantitative phenotypes are integrated with other genetic, genomic, and biological data in mgi. Transcriptome profiling with microarrays thermo fisher. The fantom5 integrated mirna expression atlas shows the expression patterns of mirnas profiled by sequencing short rna libraries obtained from human and mouse samples. Id like to find gene expression data for a few different primary cell lines. The tissue atlas contains information regarding the expression profiles of human genes both on the mrna and protein level. Contained here is a new html library wherein individual gene expression profiles. In addition to an unstimulated control, cells were also incubated with lps, anticd3anticd28 antibodies, or phorbol 12myristate acetate and ionomycin. Gene expression data analysis software tools omicx. The software is available as a media or ftp request for those customers who own a valid oracle database product license for any edition. This software is really helpful, it is like you have a virtual mice colony on your screen.
Search for expression profile data from the riken mouse cdna microarray. Additionally, data were linked to several microarray gene profiles, including biogps normal tissue profiles and nci60 cancer cell line expression data. The immunological genome project is a collaborative group of immunologists and computational biologists who are generating, under carefully standardized conditions, a complete microarray dissection of gene expression and its regulation in the immune system of the mouse. Built using the latest transcriptomic knowledge from multiple sequence data sources, they. Geo is a public functional genomics data repository supporting miamecompliant data submissions. Below are the links to the predicted cisregulatory elements in each tissuecell type. Ivygap is a dataset for exploring the anatomic and genomic basis of glioblastoma. Genevestigator visualizing the worlds expression data. Transcript abundance is in many ways an extraordinary phenotype, with special attributes that confer particular importance on an understanding of its genetics. The gene expression profiles were quantified using cufflinks software version 2. This article contains data related to the research articles spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences feng et al. The data profiles are presented as an indexed and clickable list of the genes each linked to a graphical image of that gene.
All underlying images of immunohistochemistry stained normal tissues are available. Gene expression profiles of the 565 transcriptionally distinct cell populations identified across nine regions in the adult mouse brain. Search for specific profiles of interest based on gene annotation or precomputed profile characteristics. Can anyone recommend a mouse colony management software. To map promoters, we relied exclusively on the presence of h3k4me3. Expression atlas r package on bioconductor search and download prepackaged data from expression atlas inside an r session. The jackson laboratory makes no representation about the suitability or accuracy of this software or data for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software or data will not infringe any third party patents, s, trademarks, or other rights. All co expression links were evaluated for functional association by statistical assessment.
Huilei xu, ihor r lemischka, avi maayan in bmc systems biology 2010 gate. A database of mirna expression profile data across different tissues and cell lines. Diverse brain myeloid expression profiles reveal distinct. Embryonic mammalian craniofacial development is a complex process. In the experiments, 15 measurements were registered of each protein per sample mouse. Within the same species and tissue there is a very high sampletosample correlation of the normalized gene expression data. The primary transformative potential of genomewide gene expression genetics is the sheer number of traits thousands that can be. An rnaseq atlas of gene expression in mouse and rat. The protein expression data from 44 normal human tissue types is derived from antibodybased protein profiling using immunohistochemistry. In order to demonstrate the utility of beadbased cytometric assays in interrogating cytokine expression profiles, mouse splenocytes were incubated under various activating conditions.
Mgi serves as a registry for mouse strains worldwide, maintaining the authoritative nomenclature for existing strains. Mousemine is funded through a grant from the nihnhgri. Our data search interface allows an integrative detailed comparison between our rnaseq data. The jackson laboratory makes no representation about the suitability or accuracy of this software or data for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software or data will not. Gene expression profiling of aging reveals activation of a. There are 38 control mice and 34 trisomic mice down syndrome, for a total of 72 mice. Microarray, sage and other gene expression databases hsls. Access interactive, genomewide image database of gene expression in the mouse brain. The unique collection of high quality data is queried by researchers for various applications in biomarker and target discovery, diagnostics and in silico modeling.
1374 298 1449 1441 954 727 55 1114 1062 548 1242 813 591 1057 519 249 1057 1267 471 1187 87 433 1244 857 619 28 1475 857 1419 895 815 654 296 824