KBaSS Transcriptomics

This is the part of KBaSS dedicated to Transcriptomics.

GxDB

This section lists the functionalities imported from GxDB. New tools will be added to this list.
  • GxDB GraphManager from Guillaume Berthommier allows you to create RadarGraphs.
    It offers other options such as probesets selection and ordering, change names, etc.

Profile Similarity

Available to registered user only.


Splicing external links

  • U12DB
    The U12 Intron Database (U12DB) aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other. The database can be queried on their Web page

KBaSS Transcriptomics External Links

  • Gene expression across adult retinal cell types (ROSKA)
    A public repository for the data from the study Transcriptional code and disease map for adult retinal cell types.
  • Mouse Retina SAGE Library (CEPKO)
    Public repository presenting the data from Blackshaw et al. 2004.
  • Retina Central (WEBER)
    An integrated platform for gene-related information on the adult mammalian retina.
  • Retinal Express
    The Mouse E14.5 Retina cDNA/EST Database.
  • NEIbank: Genomics and bioinformatics resources for vision research.
    NEIBank is a database of assembled EST data from eye tissue libraries.
  • RNA-Seq unified mapper (RUM)
  • MiRNEye
    MiRNEye is a high-resolution expression atlas revealing the spatiotemporal distribution of 221 miRNAs in the developing and adult wild-type mouse eye.
  • RP gene expression atlas
    RP gene expression atlas is a database of RNA expression profiles obtained by RNA in situ hybridization of genes responsible for Retinitis Pigmentosa both in human and mouse adult eye sections.
  • GeneNetwork
    GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes.
  • Braincloud
    BrainCloud is a freely-available, biologist-friendly, stand-alone application for exploring the temporal dynamics and genetic control of transcription in the human prefrontal cortex across the lifespan.
  • Allen Brain Atlas
    Allen Brain Atlas is a growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools.
  • Brain RNA-Seq
    An RNA-Seq transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.
  • ESEfinder
    ESEfinder: a web resource to identify exonic splicing enhancers.
  • Single-cell analysis of mouse cortex
    Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
  • The Human Transcription Factors
    The HumanTFs website displays the results of scanning and curating 2765 putative TF proteins, with a separate page for each TF, along with all known motifs and information and sequence alignments for each DNA-binding domain type.
  • National Eye Institute Commons
    The NEI Commons is a virtual infrastructure to enable sharing. The Commons portal provides a platform for querying and accessing vision research data and tools for data processing and analysis.
  • Single Cell Portal
    Visualization portal for single cell RNA-seq data.
  • Cancer Cell Line Encyclopedia
    The CCLE (Cancer Cell Line Encyclopedia) project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification.
  • The Cancer Genome Atlas
    The Cancer Genome Atlas (TCGA), a collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), has generated comprehensive, multi-dimensional maps of the key genomic changes in 33 types of cancer.
  • Genotype-Tissue Expression Portal
    The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation.
  • Hippocampus RNA-seq atlas
    This atlas allows to interactively analyze and visualize RNA-seq data for all excitatory cell populations in the hippocampus at multiple levels of granularity.
  • 4D Retinal Nucleome Initiative
    PeCan provides interactive visualizations across various projects at St. Jude Children's Research Hospital and its collaborating institutions.
  • Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution
    Single cell RNA Seq data from the article https://doi.org/10.1016/j.cell.2020.08.013
  • GEO: a public functional genomics data repository supporting MIAME-compliant data submissions.

    GEO Datasets:
    • GSE33134: Protective gene expression changes elicited by an inherited defect in photoreceptor structure.
    • GSE29801: Systems-level analysis of age-related macular degeneration reveals global and subtype-specific functional pathways.
    • GSE24512: Expression variation in the mouse retina.
    • GSE24423: Transcriptomic characterization of the diabetic retinal response to chronic insulin treatment.
    • GSE21900: Expression profiling of the Otx2 CKO retina.
    • GSE16974: Retinal gene expression in Egr-1 knock-out mice during development (p30 and p42).
Frédéric Blond