Useful Links Cape Biology



Coffee Addiction
Effects of Fertilisers, Manure and Polythene on therate of elongation of the Hypocotyl
The Effect of Oil Spills on Oceans
Harmful Effects of Mobile Radiation
On Recent Diseases - Ebola
What is the Best Way to Disinfect a Toothbrush
Erasing and Implanting Human Memory
Does Price and Vitamin C Affect How Fast Fruits Rot
Strawberry DNA Extraction
Sickle Cell Anemia and its Prevention
How Does Mold Grow
How Does Microwave Radiation Affect Different Organisms
What Effect Does Glucose Have on the Longevity of Cut Flowers
Diffusion VS Food Coloring
Microwave and Germination of Seeds
Heart Rate and Video Games
Yeast Reproduction in Sugar Substitutes
Angina Pectoris
Pedigree Analysis
Urinalysis
Ozone Depletion
What Music Does Bacteria Enjoy the Most
How Does Light Affect Yeast
How Cigarettes Affect Your Health
Study on Probiotics and their Preparation
The Way Blood Works
Testing the toxicity of Marine Pollutants using Daphnia
Antibiotics Naturally
Effect of Cannabis on the Human Body
Eye Disorders in Children and Adolescents
Human Cloning: Another You?
Thigmotropism In Tendrils
Brush Away You Smile
Ability of Curry and Cinnamon to Inhibit Bacterial Growth
Which Cheese Grows Mold The Fastest
Using Garden Mulch to Make a Bug Zoo
Turning to Motor Learning
Eye Can See You
Can Dog Drool Kill Germs
Growing Yeast: Sugar Fermentation
Does Oregano Oil Have an Antibiotic Effect
Do Different Diets in Ruminant Animals Affect the Microorganism Colony Growth
The Effect of Alkalines and Acids on Bacterial Growth
Saving the World One Yard at a Time
Ethyl Alcohol vs. E. coli
Effectiveness of Various Spices in Promoting or Inhibiting the Spoilage Rate of Food
Measuring Human Horsepower
Does a Mouse Rely More on His Spatial Memory or Vision
Conserving Agricultural Irrigation Water by Controlling Transpiration Loss via Wind
Effects of Ocean Water as an Irrigation Supplement on the Growth of Rice Seedlings
How Does Music Affect Plant Growth
Factors Affecting Nodule Formations in Legumes
What Do Plants Need Most
Compost or Fertilizer
Effect of Sugar on Bean Plant Growth
Does the Color of Light Affect Plant Growth
Is Spinach Made in the Shade
The Speed of Sprouting Seeds
Investigating Seed Tolerance for Freezing Temperatures
Fun with Phosphorus
Comparing Varying Levels of Oxygen Aeration in Increasing Plant Production
Salt: Friend or Foe
Cattails in the Water
Cloning 101
What Angle of Impact Has the Most Effect on Making a Bruise
Ultraviolet Radiation
Do Rats Learn Faster with Peer Pressure
Can You Make the Grade
Effects of Reading and Working on the Computer on Vision
Blowing Off Carbon Dioxide
Are Fingerprints Hereditary
Effect of the Timing of the Application of Potassium on Antirrbinum
Determining the Effects of Water Temperature and Exposure Terms on Seed Germination
Effect of Color on Cherry Trees
Hydroponics and Aeroponics
Suck It Up
Phytoremediation of Zinc
Comparison of the Effectiveness of Organic Worm Castings
Is It All Downhill from Here
Sunless Sunflowers
Does Greater Leaf Diameter Increase Transpiration Rate of Rose Geranium
Physiology of Plants in a Simulated Martian Atmosphere
Death in a Water Bath
Making of a Potpourri Fertilizer
Does Beta Carotene Prevent Tumor Growth in Plants
Growth Rate of Poa pratensis in Pure Humus
Diabetes and Exercise
The Power of Rat Senses
Which Color is Dominant in Mice
Does Varying Feed Affect the Milk of Lactating Caprines
Are Mice Territorial
Bioartificial Engineered Heart Tissue
Effects on the Flow Rate, as a Representation of Stroke Volume
Maintaining Correct Balance
Effects of Diet on Blood Glucose
Ammonia: The Passed Gas
Do the Right and Left Ears Hear Notes Differently
Got Stamina?
Do You Hear What I Hear
Blood Pressure
Nail-Patella Syndrome Phenotype Expression
Effect of Pupil Dilation on Peripheral Vision
Now You See It, Now You Don't
Effect of Exercise on Blood Pressure and Pulse Rate
Effects of Various Aromas on Animal Behavior
Effect of Ingested Fluid Temperature on Basal Body Temperature in Humans
Family Fingerprints
To Chew or Not to Chew
Does Blood Pressure Affect Heart Rate
Retinal Glare Recovery
Whose Mouth Is Cleaner
How Fibonacci Is Your Face
Get a Head Start II
Doggy Vision
There's a Germ Out There
Effects of Different External Factors in Changing the Effectiveness of Various Antibiotics
Can I Eat That
Demolishing Dental Bacteria
Kimchi, Spicy Korean Culture
Staph Aureus
Does the Surface Clarity of Plastic Bottles Affect Solar Water Disinfection
Effects of Temperature on Bacterial Pigmentation
Do Bacteria Like Gasses
Study of the Effects of Green Tea on Oral Bacteria
Mystery Behind Bacteria Levels in Gym Equipment
Fungus Among Us
Yeast Past Its Code Date
Meat That's Raw
pH Tolerance of Microbes
Which Ground Beef Has the Least Bacteria
Do Different Dilutions of Disinfectants Affect the Development of Bacterial Resistance
Isolation of Staphylococcus aureus from Raw and Pasteurized Milk
Is Garlic Antibacteria
How Much Bacteria Is on Your Retainer
What Is the Best Way to Clean Your Toothbrush
Study of Bacteria Growth in Varying Acidic Environments
Which Acne Medications Are Most Effective
Beleaguered Beef
Study of the Health Benefits of Spicy Cooking
What Are the Effects of Ultraviolet Light on Bacteria Mortality
The Five Second Rule
Bacteria Affected by Ultra-Violet Light

Nucleotide and Protein Sequences

  • 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

Genome Browsers

  1. Synthetic Biology Tools - links to online tools that are related to Synthetic Biology. Gene and protein analysis programs and databases GMOD - a collection of open source software tools for managing, visualising, storing, and disseminating genetic and genomic data.
  2. Find the help you need with your biology homework! Access answers to several hundred biology questions, carefully explained and easy for you to understand.

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. A website mainly aimed at students studying A-Level Biology - covers genetics, cells, biochemistry, enzymes, ecology, environment, photosynthesis, respiration, heart.

  • 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

Useful Links Cape Biology Syllabus

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

Multiple
  • 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

  • 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

Useful Links Cape Biology Impact Factor

Signaling pathways

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

Protein phosphorylation

  • 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

Useful Links Cape Biology Multiple Choice

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

Useful Links Cape Biology Key

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