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Guide to the Human Genome

Subject Area(s):  GenomicsHandbooks

By Stewart Scherer

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© 2011 • 1,008 pp., illus. (212 b/w), appendix, index
Paperback •
ISBN  978-0-879699-44-4

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Presenting the genes of the human genome in their biological context, Guide to the Human Genome is an extensive online resource (also available in print) that provides easy access to information about human genes and their roles in specific processes. With numerous illustrations and tables, each of the nearly 300 sections of the Guide describes genes involved in a specific pathway, process, or structure—from the molecular and cellular levels to developmental and physiological processes. In the online version, these sections contain links to more information about proteins encoded by over 17,000 known or predicted human genes. For each protein, basic characteristics about its composition and length, its human relatives and relatedness to proteins in other species, and direct links to resources at NCBI are included. Additional links to NCBI resources are provided for human noncoding RNAs and repeated DNA elements and for proteins of interest from other species. The entire text of the Guide is searchable, and tools are available for identifying human protein sequences using those from other species. The Guide will be useful to researchers looking to connect sequence data with functional information, and can be used in parallel with traditional texts in undergraduate and graduate courses to provide a genomics dimension and experience of identifying genes underpinning processes of interest.


1. Introduction
Reference Protein Set
Data Sets for Comparative Genomics
About the Figures
Searching Gene Names or Descriptions
Protein Searches with BLASTP
Searching the Text
2. Exploring the Genome
Chromosomes and DNA (includes the mitochondrial genome)
Noncoding RNAs
Gene Structure
Protein Composition and Structure
Domain Structure of Proteins
Gene Families
Comparative Genomics
Additional Reading
3. Metabolism
Metabolism and Evolution
Hexokinases and Initial Sugar Metabolism
Glycolysis (includes gluconeogenesis)
TCA Cycle
Oxidative Phosphorylation (includes the electron transport chain)
Pentose Phosphate Pathway
Galactose and Lactose
N-Acetyl Sugars and Hyaluronan
Alcohol and Aldehyde Dehydrogenases
Fatty Acid Synthesis
Arachidonate, Prostaglandins, and Leukotrienes
Fatty Acid Oxidation and Ketone Bodies
Lipid Metabolism
Sphingomyelin, Ceramides, and Glycolipids
Cholesterol Biosynthesis
Steroid Hormones
Bile Acids and Other Cholesterol Derivatives
Amino Acid Biosynthesis and Selected Derivatives
Amino Acid Catabolism
Urea Cycle, Nitric Oxide, and Polyamines
Pyrimidine Biosynthesis and Catabolism (includes salvage pathways)
Purine Biosynthesis and Catabolism (includes salvage pathways)
Nucleotide Pathways
Pteridines and Molybdopterin
Vitamin Pathways, Coenzymes, and 1-Carbon Metabolism
Cytochrome P450 Enzymes (includes diflavin oxidoreductases)
Phosphatases and Sulfatases
Glutathione Pathways (includes related redox reactions)
Xenobiotic Pathways
Additional Enzymes and Related Sequences (includes cytochrome b5 and the α / β hydrolase fold family)
Additional Reading
4. DNA Replication, Recombination, Repair, and Chromatin
DNA Replication Systems
DNA Polymerases
Replication Proteins
Telomere Functions
DNA Methylation
DNases, Recombination, and DNA Repair
DNA Transposon and Retrovirus-related Sequences (includes LINE and SINE elements)
Histones, Related Proteins, and Modifying Enzymes
Nonhistone Chromosomal Proteins (includes protamines, transition proteins, HMG proteins, chromodomain family)
Centromere Proteins
Additional Reading
5. Transcription and RNA Processing
RNA Metabolism
RNA Polymerase and General Transcription Factors
Small RNAs in RNA Processing
Capping and Splicing
RNA Editing and Other RNA Modifications
RNases and RNA Stability
DEAD / H Helicase Family
RNA-binding Proteins
Additional Reading
6. Translation and Protein Modification
Translation and Modification Systems
Codon Usage
tRNA Enzymes
Translation Factors
Selenium Proteins
Protein Glycosylation (includes transferases involved in synthesis of glycolipids)
GPI Anchoring
Prenylation and Related Modifications
Peptidylprolyl Isomerases
polyADP-Ribose Polymerase Family
Additional Protein Modifications (includes repair reactions)
Additional Reading
7. Proteases
Overview of the Proteases
Serine Proteases
Cysteine Proteases
Aspartic Proteases
Peptide-processing Enzymes
Protease Inhibitors
Ubiquitin and Related Protein Modifications
Cullins and SCF Complexes (includes VHL pathway)
Additional Reading
8. Structural Proteins
Origins of Structural Proteins
Actin and Related Proteins
Tubulin and Microtubules
Dynein and Dynactin
Late Cornified Envelope Family
Spectrin and Plectin Families
Ankyrin Family
Kelch Family
Additional Structural Proteins (includes IFT proteins)
Additional Reading
9. Protein Interaction Domain Families
Domains, Motifs, and Composition
LIM Domain Proteins
PDZ Domain
WD Repeat Proteins
Ring Finger Proteins
Tripartite Motif Family
Zinc Finger Proteins
Bromodomain Family
Leucine-rich Repeat Family
Coiled-Coil Proteins
Tetratricopeptide Domains
WW Domain
Additional Interaction Domain Families (includes IQ, sterile α, COMM, DEP, Tudor, BTB, EH, sushi, DENN, RUN, LEM)
Additional Reading
10. Stress Response and Homeostasis
Conservation of Stress Responses
Heat-Shock Proteins and Chaperonins
Oxygen Sensing and Hemoglobin
Solute Carrier Families (membrane transporters)
ATP-binding Cassette Proteins
Iron, Copper, and Arsenic Metabolism
Oxysterol-binding Protein Family
Carbonic Anhydrases
Sodium, Potassium, and Calcium Membrane ATPases
Amphipath-transporting ATPase Family
Additional Stress Response Functions
Additional Reading
11. Signals
Signaling Pathways and Microbial Pathogenesis
G-Protein-coupled Receptors
Peptide and Protein G-coupled Signals
G Proteins
Inositol Pathways (includes protein kinase C)
Rho and Rac
Ran and Rag
ADP-Ribosylation Factors
Additional Guanine Nucleotide-binding Proteins
Cyclic Nucleotides
Calmodulin and Calcium
TNF and Related Signals (includes NGF)
Receptor Tyrosine Kinases
Non-Receptor Tyrosine Kinase Pathways
Protein Tyrosine Phosphatases
MAP Kinase Pathways
Additional Serine / Threonine Protein Kinases
Serine / Threonine Protein Phosphatases
Protein Kinases
CREB / ATF Family
Jun / Fos Complexes
NF-κB Pathway
mTOR Pathway
Nucleotide and Nucleoside Receptors
Integrins (includes tetraspanins)
Netrins and Laminins
Fibronectin Family
14-3-3 Proteins
BCL2 Pathways, Caspases, and Programmed Cell Death
Nuclear Receptors
Additional Signal Responses
Additional Reading
12. Cell Structure and Organelles
Partitioning and Organelles
Nucleus and Nucleolus
ER, Golgi, and the Secretory Pathway (includes endosome traffic)
Lysosomes and Related Organelles
Gap Junctions and Tight Junctions
Additional Membrane Functions (includes autophagy, lipid transfer, dynamin family, scavenger receptors, lipid rafts, endocytosis)
Additional Reading
13. Cell Cycle
Eukaryotic Cell Cycle Control
Cyclins and Related Functions
Myc and Related Functions
p53 Pathway
RB1 and Related Functions
E2F Pathways
Anaphase-promoting Complex
Spindle, M phase, and Meiosis
Additional Cell Cycle Functions (includes other CDC genes, growth arrest genes)
Additional Reading
14. Development
Gene Families and Development
Stem Cells and Early Development
Left�Right Axis
Hedgehog and Related Pathways
Notch Pathway
Wnt Signals
Planar Cell Polarity (includes Bardet�Biedl syndrome loci and cilia formation)
Homeobox and Related Proteins
HOX Genes
FOX Family
SOX Family
POU Domain
T Box Family
PHD Finger Proteins
Krüppel-related Zinc Finger Proteins
Helix-Loop-Helix Transcription Factors
Ephrins and Ephrin Receptors
Epidermal Growth Factor
Fibroblast Growth Factors
TGF-β Family
Growth Hormone and Related Hormones
Cadherins and Related Proteins
Melanoma Antigen Family
Hematopoiesis and Erythrocytes
Ets Family
Additional Genes in Development (includes MAF family, doublesex-related proteins, AP-2 transcription factors, MEF family, tubby family, Sprouty family, carcinoembryonic antigen family, thrombospondin repeat family, MAM domain, chordin family, EYA family, retinoic acid, LY6 family, immunoglobulin-related proteins)
Noncoding RNAs and Development
Additional Reading
15. Organs and Tissues
Organs and Hormones
Extracellular Matrix
Bone and Related Tissues (includes parathyroid functions)
Skin and Related Tissues
Thyroid and Thyroid Hormone Receptor
Adipose Tissue
Cardiovascular System
Lacrimal and Salivary Glands
Pancreas and Insulin (includes insulin receptor)
Stomach, Small Intestine, and Colon
Kidney (includes bladder)
Testes and Sperm
Mammary Tissues
Ovary, Uterus, and Placenta
Additional Reading
16. Nervous System
Gene Families and the Nervous System
Sodium Channels (includes voltage-gated proton channel)
Potassium Channels
Calcium and TRP Cation Channels
Chloride Channels
GABA and Glycine
Serotonin (includes melatonin)
Olfactory Receptors
Taste Receptors
Auditory and Vestibular Functions
Photoreceptors and Related Functions
Crystallins and Other Eye Proteins
Oligodendrocytes and Myelin
Circadian Rhythms
Additional Brain Proteins (includes β amyloid, Huntington�s disease, prion protein, fragile X)
Additional Reading
17. Host Defense
Innate and Adaptive Immunity
Lectin Families
Toll-like Receptors
Pyrin and Associated Functions
Fc Receptors
MS4 Family
Superoxide Pathway
HLA and Related Proteins
Additional Immunoglobulin-related Receptors (includes NK cell receptors)
Butyrophilin Family
Interleukins and Their Receptors
Chemokines and Their Receptors
Macrophages and Monocytes
Neutrophils, Eosinophils, and Basophils (includes mast cells)
T cells (includes thymus)
B cells
Platelets and Megakaryocytes (includes PDGF receptor)
Additional Host Defense Functions (includes cytosine deaminase-related enzymes, selectin family, C-reactive protein family, secretoglobins, defensins, peptidoglycan recognition family)
Additional Reading
Retroviral Oncogene Homologs
Y-linked Genes
Major Disease Loci
Common Drug Targets
Viral Receptors
Proteins Measured in Common Diagnostic Tests
Additional Conserved Proteins
Proteins Absent from the Reference Set
Additional Reading
Gene index

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