Nencki Institute - Laboratory of Bioinformatics
BIOINFO LAB


Publications
  • PubMed
  • gopubmed

    Functional analysis:
  • gProfiler - a web server for functional interpretation of gene lists.
  • DAVID - The Database for Annotation, Visualization and Integrated Discovery.
  • GSEA - Gene Set Enrichment Analysis

    Information about genes and pathways:
  • GeneCards - searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes.
  • KEGG - KEGG: Kyoto Encyclopedia of Genes and Genomes
  • WikiGenes - is a non-profit initiative to provide a global collaborative knowledge base for the life sciences, where authorship matters.
  • Ensembl - genome databases for vertebrates and other eukaryotic species, and makes this information freely available online
  • UCSC - contains the reference sequence and working draft assemblies for a large collection of genomes
  • Ingenuity Target Explorer
  • PANTHER - consists of over 177, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components
  • REACTOME - a curated pathway database
  • BioCyc - is a collection of 7600 Pathway/Genome Databases (PGDBs), plus software tools for understanding their data
  • UniProt - resource of protein sequence and functional information
  • ArrayExpress - Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.

    miRNA
  • miRTarBase - the experimentally validated microRNA-target interactions database
  • miRNEST - an integrative microRNA resource
  • miRBase - the microRNA database
  • EpimiRBase - a comprehensive database of microRNA-epilepsy associations
  • miRSearch - Exiqon - to find microRNAs, genes, diseases and tissues
  • FireFly - lets you find the most important microRNAs for your research
  • miRSel - Automated extraction of associations between microRNAs and genes from the biomedical literature
  • Phenomir - provides information about differentially regulated miRNA expression in diseases and other biological processes.
  • DIANA - miRNA target, pathways, etc
  • starBase - designed for decoding Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data and tumor samples (14 cancer types, >6000 samples)
  • TargetExpress - miRNA target prediction with gene expression profiles

    Tissue & Cell specificity database
  • Rat BodyMap - a database for a rat expression profiles on RNA-Seq
  • BIOGPS - gene annotation portal - information about tissue/organ specificity
  • The Human Protein Atlas - a protein expression database
  • Brain RNA-Seq - a database for a brain cells gene expression
  • HippoSeq - a comprehensive RNA-seq database of gene expression in hippocampal principal neurons
  • A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes - publication, data in supplements
  • TiSGeD - Tissue-Specific Genes /is not longer under maintaince/
  • PaGenBase - is a free database that provides information of pattern genes (specific genes, selective genes, housekeeping genes and repressed genes) of 11 model organisms
  • TiGER - Tissue-specific Gene Expression and Regulation
  • Browse Brain Cell - tools
  • DeCoN - The Developing Cortical Neuron Transcriptome Resource

    Circular RNA
  • circBase - circular RNA database

    Drug targets
  • DrugBank - is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information

    Circadian rythms
  • CircaDB - Circadian Expression Profiles Data Base

    Data resources:
  • GEO - a public functional genomics data repository

    Epilepsy related databases
  • CarpeDB - CarpeDB, a dynamic epilepsy genetics database
  • epiGAD - The Epilepsy Genetic Association Database (epiGAD) is an online repository of data relating to genetic association studies in the field of epilepsy.
  • EpimiRBase - a comprehensive database of microRNA-epilepsy associations

    Other - tools and blogs
  • RNA-Seq Blog
  • R-bloggers
  • SEQanswers
  • Bioconductor
  • CRAN
  • BitBucket
  • GitHub
  • RStudio
  • BEDOPS - the fast, highly scalable and easily-parallelizable genome analysis toolkit
  • bedtools - a powerful toolset for genome arithmetic
  • Circos - Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.
  • PTBI - Polskie Towarzystwo Bioinformatyki
  • BioInfoWorld - Koło Naukowe Bioinformatyki UJ
  • CopyRight: Konrad J. Dębski 2015 - 2017