Table 4

SGD8 gene clusters. Clusters obtained from the SGD8 dataset.

Cluster (num. genes)

Majority Slim annotation

Comments


A. DNA repair and replication (108 genes)

'DNA metabolism' (103 genes)

The rest of the genes in the cluster (5) are also related to DNA repair and replication processes taking into account their functional annotations in SGD.

B. Lipid metabolism (38 genes)

'lipid metabolism' (32 genes)

Genes annotated with other Slim categories (6), also contain functional annotations in SGD revealing their implication in lipid metabolism.

C. Response to stress (46 genes)

'response to stress' (23 genes)

Among genes with other Slim categories there are genes involved in the ubiquitin-dependent protein catabolism (GRR1, SKP1, CDC4, MET30, CDC34, CDC53, HRT1, UFD1, CDC48, RPN4, DOA1); chaperones (SIS1, SSB1, YDJ1, SSA1) and RAS protein signal transduction (RAS1, IRA2, CDC25).

D. Transport I (47 genes)

'transport' (37 genes)

Most genes in the cluster (40) are annotated with membrane related localizations in GO cell component category: 'plasma membrane' (35 genes), 'periplasmic space' (4 genes) and 'membrane fraction' (1 gene).

E. Transport II (25 genes)

'transport' (20 genes)

13 genes correspond to hydrogen-transporting V-type ATPases (namely STV1, VMA2, VPH1, VMA13, VMA8, VMA7, VMA5, TFP3, VMA6, VMA10, VMA4, TFP1, PPA1). It also other 'transport' category proteins: four members of the P-type ATPase superfamily (PMC1, PMR1, ENA1, PMA2), and three ion channels (CCH1, MID1 and FPS1).

F. Transport III (51 genes)

'transport' (42 genes)

Non-transport genes are related to vacuole organization and inheritance (FAB1, TRX1, TRX2) or glycosylation (MNN4, KRE2, WBP1).

G. Mitochondria (30 genes)

'transport' (24 genes)

Contains mitochondria located genes. Transport genes: members of the mitochondrial protein translocase family (TIM22, MRS11, TIM13, TIM8, TIM9, TIM17, MAS6, TOM40, TIM44, MGE1, TOM70, TOM20, TOM5, TOM22, TOM6, TOM7 and MRS5); mitochondrial outer membrane porin (POR1), translocase of the mitochondrial inner membrane (OXA1). Non-transport genes are located in the 'mithocondrial matrix' (SSQ1, HSP78, PIM1, PET54), 'mitochondrial inner membrane' (PET111) and 'mitochondrion' (MTF2).

H. Gene expression (chromatin) (33 genes)

'DNA metabolism' (28 genes)

All genes contain chromatin related GO annotations in SGD. Contains 5 genes with other Slim categories related to chromatin.

I. Cell cycle (37 genes)

'cell cycle' (33 genes)

Contains also 'transport' and two "signal transduction" Slim genes. Transport genes are: MAD1 (annotated as mitotic spindle checkpoint) and PDS1 (essential for cell cycle arrest in mitosis in the presence of DNA damage or aberrant mitotic spindles).

J. mRNA and protein biosynthesis (93 genes)

'protein biosynthesis' (40 genes)

Other genes in the cluster include translation elongation and translation initiation factors as well as those involved in mRNA processing like mRNA catabolism, mRNA-nucleus export or the RNA polymerase II transcription machinery (e.g. regulators like CDC36, CDC39).

K. Cell morphology response (67 genes)

'cell wall organization and biogenesis' (25 genes)

Among them a significant number is related to cell shape and structure (cell wall and cytoskeleton), as well as events and processes related to morphological changes in the cellular envelope (cell budding, sporulation, conjugation with cellular fusion, endocytosis).


Chagoyen et al. BMC Bioinformatics 2006 7:41   doi:10.1186/1471-2105-7-41

Open Data