Bioinformatics and Functional Genomics

Table 8-1. Definitions from the InterPro database of protein families and related terms (adapted from http://www.ebi.ac.uk/interpro/user_manual.html).

Term	Definition
Family	An InterPro family is a group of evolutionarily related proteins that share one or more domains/repeats in common. A InterPro entry of type=family may contain a signature for a small conserved region that is representative of the family, and need therefore not necessarily cover the whole protein.
Domain	An InterPro domain is an independent structural unit which can be found alone or in conjunction with other domains or repeats. Domains are evolutionarily related. An InterPro entry of the type=domain is diagnostic for a domain but not necessarily define domain boundaries exactly.
Repeat	An InterPro repeat is a region that is not expected to fold into a globular domain on its own. For example 6-8 copies of the WD40 repeat are needed to form a single globular domain. There also many other short repeat motifs that probably do not form a globular fold that have type=repeat.
Post-translational modification	A post-translational modification includes for example, an N glycosylation site. The sequence motif is defined by the molecular recognition of this region in a cell. This may group together proteins that need not be evolutionarily related.

 

Table 8-2. Definitions of protein domains and motifs from the SMART database (adapted from http://smart.embl-heidelberg.de/help/smart_glossary.shtml). SMART is a tool to allow automatic identification and annotation of domains in user-supplied protein sequences (see Chapter 10).

Term	Definition
Domain	Conserved structural entities with distinctive secondary structure content and a hydrophobic core. In small disulphide-rich and Zn2+-binding or Ca2+- binding domains the hydrophobic core may be provided by cystines and metal ions, respectively. Homologous domains with common functions usually show sequence similarities.
Domain composition	Proteins with the same domain composition have at least one copy of each of domains of the query.
Domain organization	Proteins having all the domains as the query in the same order (additional domains are allowed).
Motif	Sequence motifs are short conserved regions of polypeptides. Sets of sequence motifs need not necessarily represent homologues.
Profile	A profile is a table of position-specific scores and gap penalties, representing an homologous family, that may be used to search sequence databases (Bork and Gibson, 1996).

 

Table 8-3. Fifteen most common domains of Homo sapiens. From the European Bioinformatics Institute (EBI) proteome analysis site (http://www.ebi.ac.uk/proteome/)(August, 2002), based upon the InterPro database (http://www.ebi.ac.uk/interpro/index.html).

InterPro ID	Matches per genome	Number of proteins	Name
IPR000822	30034	1093	Zn-finger, C2H2 type
IPR003006	2631	1032	Immunoglobulin/major histocompatibility complex
IPR000561	4985	471	EGF-like domain
IPR001841	1356	458	Zn-finger, RING
IPR001356	2542	417	Homeobox
IPR001849	1236	405	Pleckstrin-like
IPR000504	2046	400	RNA-binding region RNP-1 (RNA recognition motif)
IPR001452	2562	394	SH3 domain
IPR002048	2518	392	Calcium-binding EF-hand
IPR003961	2199	300	Fibronectin, type III
IPR001478	1398	280	PDZ/DHR/GLGF domain
IPR005225	261	261	Small GTP-binding protein domain
IPR000210	583	236	BTB/POZ domain
IPR001092	713	226	Basic helix-loop-helix dimerization domain bHLH
IPR002126	5168	226	Cadherin

 

Table 8-4. Some physical properties of proteins. Abbreviations: G protein, GTP-binding protein; nAChR, nicotinic acetylcholine receptor.

property	Classical method	Example
amino acid motifs		PDZ domain (e.g. nitric oxide synthase), coiled coil domain (e.g. hemagglutinin, syntaxin, SNAP-25, myosin)
isoelectric point (pI)	derived from isoelectric focusing
molecular weight	derived from Stokes radius and sedimentation coefficient
posttranslational modifications: phosphorylation	Enzymatic analyses	synapsin
posttranslational modifications: glycosylation	Enzymatic analyses	nerve growth factor, neural cell adhesion molecule
posttranslational modifications: isoprenylation		lamin B, G protein g subunits, rab3A
posttranslational modifications: palmitoylation		b-adrenergic receptor, GAP-43, insulin receptor, rhodopsin, nAChR
posttranslational modifications: myristoylation		PKA, Gia-subunit, MARCKS protein, calcineurin
posttranslational modifications: GPI-anchored proteins	Enzymatic analyses	alkaline phosphatase, thy-1, prion protein, 5’-nucloetidase, uromodulin
sedimentation coefficient	derived from sucrose density gradients
Stokes radius	derived from gel filtration
transmembrane domain	derived from subcellular fractionation

 

Table 8-5. Participating organizations and databases in the Gene Ontology Consortium. Adapted from http://www.geneontology.org/.

Database or organization	Organism	Common name
Berkeley Drosophila Genome Project	Drosophila melanogaster	Fly
Compugen
DictyBase	Dictyostelium discoideum	slime mold
European Bioinformatics Institute (EBI)	Various
FlyBase	Drosophila melanogaster	Fly
Genome Knowledge Base (GKB) at Cold Spring Harbor Laboratory	Various
Gramene	Oryza sativa; other grains, monocots	Rice
Mouse Genome Database (MGD) & Gene Expression Database (GXD)	Mus musculus	Mouse
Pathogen Group at the Wellcome Trust Sanger Institute	Various
PomBase	Schizosaccharomyces cerevisiae	Fission yeast
Rat Genome Database (RGD)	Rattus	Rat
Saccharomyces Genome Database (SGD)	Saccharomyces cerevisiae	Baker’s yeast
The Arabidopsis Information Resource (TAIR)	Arabidopsis thaliana	Thale cress
The Institute for Genomic Research (TIGR)	Various
WormBase	Caenorhabditis elegans	Worm

 

Table 8-6. Web sites useful to access Gene Ontology data.

Browser	Description
AmiGO from BDGP	A GO browser from the Gene Ontology Consortium
MGI GO Browser	From the Mouse Genome Informatics web site at the Jackson Laboratories
“QuickGO” at EBI	From the EMBL and European Bioinformatics Institute; integrated with InterPro (Chapter 10)
EP GO Browser	A GeneOntology browser and analysis tool that is part of the Expression Profiler suite at the European Bioinformatics Institute
CGAP GO Browser	From the Cancer Gene Anatomy Project at the NIH

 

Table 8-7. Evidence codes for the Gene Ontology project. Adapted from http://www.geneontology.org/.

Abbreviation	Evidence code	Example(s)
IC	Inferred by curator	A protein is annotated as having the function of a “transcription factor.” A curator may then infer that the localization is “nucleus”
IDA	Inferred from direct assay	An enzyme assay (for function); immunofluorescence microscopy (for cellular component)
IEA	Inferred from electronic annotation	Annotations based on “hits” in searches such as BLAST (but without confirmation by a curator; compare ISS)
IEP	Inferred from expression pattern	Transcripts levels (e.g. based on Northern blotting or microarrays) or protein levels (e.g. from Western blots)
IGI	Inferred from genetic interaction	Suppresors; genetic lethals; complementation assays; experiments in which one gene provides information about the function, process, or component of another gene
IMP	Inferred from mutant phenotype	Gene mutation; gene knockout; overexpression; antisense assays
IPI	Inferred from physical interaction	Yeast two-hybrid assays; copurification; co-immunoprecipitation; binding assays
ISS	Inferred from sequence or structural similarity	Sequence similarity; domains; BLAST results that are reviewed for accuracy by a curator
NAS	Non-traceable author statement	Database entries such as a SwissProt record that does not cite a published paper
ND	No biological data available	Corresponds to “unknown” molecular function, biological process, or cellular compartment
TAS	Traceable author statement	Information in a review article or dictionary

 

Table 8-8. Functional assignment of proteins based upon their enzymatic activity: partial list of the Enzyme Commssion (EC) classification system (release 27.0, October 2001). From http://kr.expasy.org/cgi-bin/enzyme-search-cl.

EC number	Description of class	# enzymes	Example of subclass
1.-.-.-	Oxidoreductases	1,003
1.1.-.-			Acting on the CH-OH group of donors
1.2.-.-			Acting on the aldehyde or oxo group of donors
2.-.-.-	Transferases	1,076
2.1.-.-			Transferring one-carbon groups
3.-.-.-	Hydrolases	1,125
4.-.-.-	Lyases	356
5.-.-.-	Isomerases	156
6.-.-.-	Ligases	126

 

Table 8-9. Functional classification of proteins in the Clusters of Orthologous Groups (COGs) database (http://www.ncbi.nlm.nih.gov/COG/)(September, 2002).

General category	Function	COGs	domains
Information storage and processing
	Translation, ribosomal structure and biogenesis	217	6,449
	Transcription	133	5,442
	DNA replication, recombination and repair	184	5,337
Cellular processes
	Cell division and chromosome partitioning	32	842
	Posttranslational modification, protein turnover, chaperones	109	3,155
	Cell envelope biogenesis, outer membrane	155	4,079
	Cell motility and secretion	133	3,110
	Inorganic ion transport and metabolism	160	5,112
	Signal transduction mechanisms	96	3,623
Metabolism
	Energy production and conversion	223	5,584
	Carbohydrate transport and metabolism	170	5,257
	Amino acid transport and metabolism	233	8,383
	Nucleotide transport and metabolism	85	2,364
	Coenzyme metabolism	154	4,057
	Lipid metabolism	75	2,609
	Secondary metabolites biosynthesis, transport and catabolism	62	2,754
Poorly characterized
	General function prediction only	449	11,948
	Function unknown	752	6,431

 

Table 8-10. Main categories of metabolic and regulatory pathways in the KEGG database (http://www.genome.ad.jp/kegg/). Hundreds of pathway maps are available within these categories.

Metabolic Pathways
	Carbohydrate Metabolism
	Energy Metabolism
	Lipid Metabolism
	Nucleotide Metabolism
	Amino Acid Metabolism
	Metabolism of Other Amino Acids
	Metabolism of Complex Carbohydrates
	Metabolism of Complex Lipids
	Metabolism of Cofactors and Vitamins
	Biosynthesis of Secondary Metabolites
	Biodegradation of Xenobiotics
Regulatory Pathways: Genetic Information Processing
	Transcription
	Translation
	Sorting and Degradation
	Replication and Repair
Regulatory Pathways: Environmental Information Processing
	Membrane Transport
	Signal Transduction
	Ligand-Receptor Interaction
Regulatory Pathways: Cellular Processes
	Cell Motility
	Cell Growth and Death
	Cell Communication
	Development
	Behavior
Regulatory Pathways: Human Diseases
	Neurodegenerative Disorders

 

Table 8-10. Tools to analyze protein motifs. From ExPASy (http://www.expasy.org/tools/)

Program	Comment
InterProScan	At EBI
ppsearch	At EBI
PRATT	At EBI
ProfileScan Server	At ISREC
PROSCAN (PROSITE SCAN)	At PBIL
ScanProsite tool	At ExPASy
SMART	At EMBL
TEIRESIAS	At IBM

 

Table 8-11. Web-based programs for the prediction of protein localization.

Program	Comment
ChloroP	predicts the presence of chloroplast transit peptides (cTP) in protein sequences
MITOPROT	calculates the N-terminal protein region that can support a mitochondrial targeting sequence and the cleavage site
PSORT	prediction of protein sorting signals and localization sites
SignalP	predicts the presence and location of signal peptide cleavage sites in prokaryotes and eukaryotes.
TargetP	predicts the subcellular location of eukaryotic protein sequences.

 

Table 8-12. Web servers for the prediction of transmembrane domains in protein sequences. Source: ExPASy web server. K. Hofmann & W. Stoffel (1993) Tmbase - A database of membrane spanning proteins segments Biol. Chem. Hoppe-Seyler 374,166

Program	Comment/source
DAS server
HMMTOP	Prediction of transmembrane helices and topology of proteins
PredictProtein server	Prediction of transmembrane helix location and topology
SOSUI	Classification and Secondary Structure Prediction of Membrane Proteins
TMpred
TMHMM (v. 2.0)	Center for Biological Sequence Analysis, Technical University of Denmark
TopPred2	Topology prediction of membrane proteins

 

Table 8-13. Tools to analyze primary structure features of proteins. From ExPASy (http://www.expasy.org/tools/)

Program	Source/comment
COILS	Prediction of coiled coil regions in proteins
Compute pI/Mw	From ExPASy
drawhca	Hydrophobic Cluster Analysis plot
Helical Wheel	draws an helical wheel, i.e. an axial projection of a regular alpha-helix, for a given sequence
M.M., pI, composition, titrage	MW, pI, Titration curve
Paircoil	Prediction of coiled coil regions in proteins
PeptideMass	From ExPASy
REP	Searches a protein sequence for a repeats
SAPS	Statistical Analysis of Protein Sequences

 

Table 8-14. Web resources for the characterization of glycosylation sites on proteins.

Program	Comment/source
DictyOGlyc 1.1 Prediction Server	neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins
NetOGlyc	Prediction of type O-glycosylation sites in mammalian proteins
YinOYang 1.2	produces neural network predictions for O-ß-GlcNAc attachment sites in eukaryotic protein sequences

 

Table 8-15.Tools to analyze postranslational modifications. From ExPASy (http://www.expasy.org/tools/)

Program	Comment
big-PI Predictor	GPI Modification Site Prediction
DGPI	Detection/prediction of GPI cleavage site (GPI-anchor) in a protein
NetPhos 2.0 Prediction Server	produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins
Sulfinator	Prediction of tyrosine sulfation sites

 

Table 8-16. Examples of proteins with unusually high occurrences of specific amino acids (modified from Ponting, 2001). The hydrophobic residues characteristic of transmembrane helices are from Tanford (1980).

Amino acid(s)	Proteins
C	Disulfide-rich proteins; metallothioneins; zinc finger proteins
D, E	Acidic proteins
G	Collagens
H	Hisactophilin; histidine-rich glycoprotein
W, L, P, Y, L, V, M, A	Transmembrane domains
K, R	Nuclear proteins (nuclear localization signals)
N	Dictyostelium proteins
P	Collagens; filaments; SH3/WW/EVHI binding sites
Q	Proteins encoded by genes mutated in triplet repeat disorders (Chapter 17)
S, R	Some RNA-binding motifs
S, T	Mucins; oligosaccharide attachment sites
abcdefg	Heptad coiled coils (a and d are hydrophobic residues) e.g. myosins

 

Table 8-17. Web-based databases of protein-protein and protein-ligand interactions.
http://dip.doe-mbi.ucla.edu/dip/Search.cgi. Some of these databases are listed in Schächter (2002).

Database	Comment
BIND (The Biomolecular Interaction Network Database)	database designed to store full descriptions of interactions, molecular complexes and pathways.
Cellzome
DIP (The Database of Interacting Proteins)
DLRP (Database of Ligand-Receptor Partners)	database of protein ligand and protein receptor pairs that are known to interact with each other
FlyBase	See Jacq (2001)
FlyNets	See Jacq (2001)
KEGG (Kyoto Encyclopedia of Genes and Genomes)
GeNet (Gene Networks database)	See Jacq (2001)
ProNet	From Doubletwist, Inc. and Myriad Genetics
STKE (Signal Transduction Knowledge Environment)	See Jacq (2001)
Transfac (Transcription factor database)
YPD, PombePD, WormPD	Proteome, Inc. databases