Guide to the Human Genome

Guide to the Human Genome

Subject Area(s): Genomics; Handbooks

By Stewart Scherer

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© 2011 • 1,008 pp., illus. (212 b/w), appendix, index
Paperback • ~~$79~~ 71.10
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.

Preface
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; Polymorphism; 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; Glycogen; 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; Heme; 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; hnRNP; Small RNAs in RNA Processing; Capping and Splicing; Polyadenylation; 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; tRNAs; tRNA Enzymes; Ribosomes; Translation Factors; Selenium Proteins; Protein Glycosylation (includes transferases involved in synthesis of glycolipids); GPI Anchoring; Prenylation and Related Modifications; Transglutaminases; Peptidylprolyl Isomerases; polyADP-Ribose Polymerase Family; Additional Protein Modifications (includes repair reactions); Additional Reading

7. Proteases: Overview of the Proteases; Serine Proteases; Cysteine Proteases; Metalloproteases; Aminopeptidases; Carboxypeptidases; Aspartic Proteases; Peptide-processing Enzymes; Protease Inhibitors; Ubiquitin and Related Protein Modifications; Cullins and SCF Complexes (includes VHL pathway); Proteasome; Additional Reading

8. Structural Proteins: Origins of Structural Proteins; Actin and Related Proteins; Myosin; Tubulin and Microtubules; Kinesins; Dynein and Dynactin; Collagen; Keratins; 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; Metallothioneins; Iron, Copper, and Arsenic Metabolism; Lipoproteins; Oxysterol-binding Protein Family; Carbonic Anhydrases; Aquaporins; 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); Ras; Rho and Rac; Rab; 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; Phosphatases; CREB / ATF Family; Jun / Fos Complexes; NF-κB Pathway; mTOR Pathway; Nucleotide and Nucleoside Receptors; Signalosome; Integrins (includes tetraspanins); Netrins and Laminins; Fibronectin Family; Semaphorins; 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; Cytoskeleton; Nucleus and Nucleolus; Centrosome; ER, Golgi, and the Secretory Pathway (includes endosome traffic); Mitochondria; Peroxisomes; 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; MicroRNAs; Additional Reading

15. Organs and Tissues: Organs and Hormones; Extracellular Matrix; Bone and Related Tissues (includes parathyroid functions); Skin and Related Tissues; Pituitary; Adrenals; Thyroid and Thyroid Hormone Receptor; Adipose Tissue; Cardiovascular System; Lung; Lacrimal and Salivary Glands; Liver; Pancreas and Insulin (includes insulin receptor); Stomach, Small Intestine, and Colon; Kidney (includes bladder); Prostate; 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; Acetylcholine; GABA and Glycine; Glutamate; Catecholamines; Serotonin (includes melatonin); Histamine; Synapses; Olfactory Receptors; Taste Receptors; Auditory and Vestibular Functions; Photoreceptors and Related Functions; Crystallins and Other Eye Proteins; Neurons; Oligodendrocytes and Myelin; Cerebellum; Hypothalamus; Circadian Rhythms; Additional Brain Proteins (includes β amyloid, Huntington’s disease, prion protein, fragile X); Muscle; Additional Reading

17. Host Defense: Innate and Adaptive Immunity; Mucins; Lectin Families; Toll-like Receptors; Pyrin and Associated Functions; Complement; Fc Receptors; MS4 Family; Superoxide Pathway; HLA and Related Proteins; Additional Immunoglobulin-related Receptors (includes NK cell receptors); Butyrophilin Family; Interleukins and Their Receptors; Interferon; Chemokines and Their Receptors; Macrophages and Monocytes; Neutrophils, Eosinophils, and Basophils (includes mast cells); T cells (includes thymus); B cells; Coagulation; 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

Appendices: 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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