Useful Links Cape Biology

Posted : admin On 8/22/2021
  1. Useful Links Cape Biology Key
  2. Useful Links Cape Biology Syllabus

Nucleotide and Protein Sequences

Useful links cape biology impact factor
  • Genbank - Nucleotide sequence database at NCBI
  • ENA - European Nucleotide Archive at EMBL-EBI
  • DDBJ - DNA Data Bank of Japan
  • Protein database at NCBI
  • UniProt - a resource of protein sequence and functional information

Genome Downloads

This eBook contains the official CAPE® Biology syllabus, effective for examinations from May/June 2008– May/June 2018 (now replaced by CXC A210/U2/17, effective for examinations from May/June 2019). If you are unsure about which syllabus you need, please contact CXC for advice. December 28th, 2017backstage. CAPE Biology Unit 2 Useful Links Your opinion please! Science in the News Field Trips Documents. This is where you will find notes, scheme of work and syllabus. Make good use of the resources posted. Please note that the syllabus is on the Unit 2 page or you can click on the link. This will give you a guide to use as we go. Cape Access is a programme that provides access to information and communication technologies (ICT) to less privileged and rural communities across the Western Cape.

Genome Browsers

  • Genome Data Viewer (NCBI)

Gene Databases

  • Gene - a gene database at NCBI
  • UniGene - a transcript database at NCBI
  • SOURCE - a gene database
  • GeneAtlas - a gene database
  • GeneCards - human gene database
  • OMIM - An Online Catalog of Human Genes and Genetic Disorders
  • AmiGo - a gene ontology database
  • HGNC - HUGO Gene Nomenclature Committee
  • GENCODE - human and mouse gene annotation database
  • Harmonizome - integrated knowledge about genes and proteins

Gene Mutations and Variations

  • dbSNP - a database of single nucleotide polymorphisms (SNPs) and small-scale insertions/deletions, microsatellites, and non-polymorphic variants
  • ClinVar - an archive of reports of the relationships among human variations and phenotypes
  • MutDB - a database for assessing the impact of genetic variants
  • HGMD - The Human Gene Mutation Database
  • GWAS Central - a centralized compilation of summary level findings from genetic association studies
  • DGV - a curated catalogue of human genomic structural variation

Gene Expression

  • Expression Atlas - gene and protein expression across species and biological conditions
  • GEO - Gene Expression Omnibus
  • ArrayExpress - data from high-throughput functional genomics experiments
  • GTEx - The Genotype-Tissue Expression Project
  • Bgee - gene expression patterns in multiple animal species
  • OmicsDI - The Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics).

Epigenetics

  • VizHub - Roadmap Epigenomics Visualization Hub
  • DeepBlue - Epigenomic Data Server
  • PubMeth - annotated and reviewed database of methylation in cancer

Gene Regulatory Elements

  • EPD - Eukaryotic Promoter Database
  • JASPAR - transcription factor binding profile database
  • ENCODE - Encyclopedia of DNA Elements
  • TRRUST - a manually curated database of human transcriptional regulatory network
  • Cistrome - integrative analysis pipelines to better mine the hidden biological insights from publicly available high throughput data
  • ChIP-Atlas - integrative and comprehensive database for visualizing and making use of public ChIP-seq data
  • GTRD - Gene Transcription Regulation Database
  • ChIPBase - a database for studying the transcription factor binding sites and motifs, and decoding the transcriptional regulatory networks of lncRNAs, miRNAs, other ncRNAs and protein-coding genes from ChIP-seq data

Non-Coding RNA Databases and Tools

  • miRBase - a searchable database of published miRNA sequences and annotation
  • miRTarBase - the experimentally validated microRNA-target interactions database
  • miRDB - online database for miRNA target prediction and functional annotations
  • TargetScan - prediction of microRNA targets
  • RNA22 - microRNA target detection
  • DIANA Tools - databases of experimentally verified miRNA targets and prediction tools
  • NONCODE - An integrated knowledge database dedicated to ncRNAs, especially lncRNAs

Protein Function and Regulation

Enzymes

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  • BRENDA - the comprehensive enzyme information system
  • MetaCyc - Metabolic Encyclopedia (enzymes, metabolites and metabolic pathways)
  • IntEnz - Integrated Relational Enzyme Database
  • ExplorEnz - the enzyme database
  • MEROPS - an information resource for peptidases
  • REBASE - The Restriction Enzyme Database

Signaling pathways

  • NetPath - manually curated resource of signal transduction pathways in humans
  • Reactome - a signaling pathway database
  • WikiPathways - a database of biological pathways

Protein phosphorylation

Useful Links Cape Biology
  • Phospho.ELM - phosphorylation site database
  • PHOSIDA - phosphorylation site database
  • dbPAF - database of phospho-sites in animals and fungi
  • PhosphoNET - human phosphosite knowledgebase
  • DEPOD - the human DEPhOsphorylation database

Protein-protein interactions

  • IntAct - a protein interaction database at EBI
  • BioGRID - a repository for interaction datasets
  • STRING - known and predicted protein-protein interactions

Protein abundance and localization

  • The Human Protein Atlas - an effort to map all the human proteins in cells, tissues and organs using integration of various omics technologies
  • PaxDb - Protein Abundance Database

Structure Databases

  • PDB - Protein Data Bank
  • CATH - a classification of protein structures from the Protein Data Bank
  • Protein Model Portal (PMP) - access to computed models and interactive services for model building
  • RNA Bricks - a database of RNA 3D structure motifs and their contacts
  • COSMIC-3D - a platform for understanding cancer mutations in the context of 3D protein structure

Small Molecules

  • Pubchem - an open chemistry database at the National Institutes of Health
  • ChEBI - Chemical Entities of Biological Interest (ChEBI), a freely available dictionary of molecular entities focused on 'small' chemical compounds
  • HMDB - The Human Metabolome Database

Cancer-related Resources

  • GDC Data Portal - platform that allows to search and download cancer data for analysis (from the TCGA and other projects)
  • COSMIC - the Catalogue Of Somatic Mutations In Cancer
  • cBioportal - visualization, analysis and download of large-scale cancer genomics data sets
  • Oncoscape - patterns and relationships between clinical and molecular factors
  • GEPIA - interactive web server for analyzing the RNA-seq data of tumors and normal samples from the TCGA and the GTEx projects
  • canSAR - an integrated knowledge-base that brings together multidisciplinary data across biology, chemistry, pharmacology, structural biology, cellular networks and clinical annotations, and applies machine learning approaches to provide drug-discovery useful predictions
  • CCLE - Cancer Cell Line Encyclopedia
  • DepMap - Cancer Dependency Map
  • GDSC - Genomics of Drug Sensitivity in Cancer

Species-specific Resources

  • MGI - Mouse Genome Informatics
  • IMPC - International Mouse Phenotyping Consortium
  • RGD - The Rat Genome Database
  • ZFIN - The Zebrafish Information Network
  • XenBase - resources related to biology of X. laevis and X. tropicalis
  • FlyBase - resources related to biology of D. melanogaster and other Drosophilidae
  • WormBase - resources related to biology of C. elegans and related nematodes
  • PomBase - a comprehensive database for the fission yeast Schizosaccharomyces pombe
  • SGD - Saccharomyces Genome Database (SGD), comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae
  • TAIR - The Arabidopsis Information Resource

Other Resources

  • Codon usage table database at HIVE