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Table 1 Examples of cross-domain GO term pairs which have a high CAS or PAS

From: Quantification of protein group coherence and pathway assignment using functional association

GO ID 1

Description

Domain

GO ID 2

Description

Domain

CAS

PAS

GO:0047077

Photinus-luciferin 4-monooxygenase activity

MF

GO:0008218

Bioluminescence

BP

697.12

0.124

GO:0009544

Chloroplast ATP synthase complex

CC

GO:0009772

photosynthetic electron transport in photosystem II

BP

232.37

0.0572

GO:0033592

RNA strand annealing activity

MF

GO:0000373

Group II intron splicing

BP

116.19

0.0367

GO:0034437

Glycoprotein transporter activity

MF

GO:0010887

negative regulation of cholesterol storage

BP

232.37

0

GO:0051636

Gram-negative bacterial cell surface binding

MF

GO:0015920

lipopolysaccharide transport

BP

348.56

0.0195

GO:0047635

alanine-oxo-acid transaminase activity

MF

GO:0019481

L-alanine catabolic process, by transamination

BP

232.37

0.3489

GO:0046812

host cell surface binding

MF

GO:0019064

viral envelope fusion with host membrane

BP

116.18

0.0756

GO:0047558

3-cyanoalanine hydratase activity

MF

GO:0019499

cyanide metabolic process

BP

697.11

0.0653

GO:0047429

nucleoside-triphosphate diphosphatase activity

MF

GO:0009149

pyrimidine nucleoside triphosphate catabolic process

BP

116.18

0

GO:0033328

peroxisome membrane targeting sequence binding

MF

GO:0045046

protein import into peroxisome membrane

BP

199.17

2.690

GO:0031499

TRAMP complex

CC

GO:0034470

ncRNA processing

BP

1.316

4.317

GO:0070531

BRCA1-A complex

CC

GO:0016579

Protein deubiquitination

BP

4.497

5.164

GO:0031252

Cell leading edge

CC

GO:0070507

regulation of microtubule cytoskeleton organization

BP

0.0097

0.0115

GO:0030893

meiotic cohesin complex

CC

GO:0000819

sister chromatid segregation

BP

0.498

0.759

GO:0043566

structure-specific DNA binding

MF

GO:0033567

DNA replication, Okazaki fragment processing

BP

0.178

0.352

GO:0042781

3'-tRNA processing endoribonuclease activity

MF

GO:0034414

tRNA 3'-trailer cleavage, endonucleolytic

BP

232.37

116.186

GO:0000816

nicotinamide riboside kinase activity

MF

GO:0034356

NAD biosynthesis via nicotinamide riboside salvage pathway

BP

348.55

104.567

GO:0001735

prenylcysteine oxidase activity

MF

GO:0030328

prenylcysteine catabolic process

BP

232.37

22.487

GO:0004121

cystathionine beta-lyase activity

MF

GO:0019279

methionine biosynthetic process from L-homoserine via cystathionine

BP

139.42

15.154

GO:0070635

nicotinamide riboside hydrolase activity

MF

GO:0034356

NAD biosynthesis via nicotinamide riboside salvage pathway

BP

348.55

27.884

  1. The table is divided into two halves with the first half containing examples of GO term pairs across different domains that have high CAS while the second half has examples with high PAS. For each of the term its description in the GO database and the domain (MF/BP/CC) where it belongs is provided. First five examples in each of the two halves are discussed in detail in the text whereas the latter five examples in each part provide missing process-function links that are detected by high CAS or PAS and are not currently linked using the part-of relationship in GO database.