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