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. 2014 Sep 11;9(9):e107036. doi: 10.1371/journal.pone.0107036

Table 2. Top 3 annotation clusters of genes downregulated in Arhgap28del bone.

Cluster componentsA p valueB Matched genesC Gene names (if annotated) of corresponding probe IDs in the GO listD
Annotation cluster 1, Enrichment score 6.72
SP_PIR_KEYWORDS secreted 4.13E–11 21 Egfl6, Hapln1, Mia1, Sfrp4, Ccl6, Col2a1, Lect1, Ptn, Matn3, Ecrg4, Matn3, Hapln1, Ccl12, Comp, C1qtnf3, Angptl1, Hapln1, Nts, Mfap5, Hapln1, Epyc, Ecrg4, Mmrn1, Cma1, Col9a1, Cxcl14
GO: 0005576∼ extracellular region 6.53E–10 22 Egfl6, Hapln1, Mia1, Sfrp4, Ccl6, Col2a1, Lect1, Ptn, Matn3, Ecrg4, Hapln1, Matn3, Ccl12, Comp, C1qtnf3, Angptl1, Hapln1, Nts, Mfap5, Matn1, Hapln1, Epyc, Ecrg4, Mmrn1, Cma1, Col9a1, Cxcl14
SP_PIR_KEYWORDS signal 1.06E–07 24 Egfl6, Mia1, Sfrp4, Ccl6, Col2a1, Snorc, Dlk1, Ptn, Matn3, Ecrg4, Matn3, Ccl12, Comp, C1qtnf3, Cd300ld, Angptl1, Nts, Mfap5, Matn1, Cpa3, Epyc, Ecrg4, Mmrn1, Cma1, Col9a1, Cxcl14
GO: 0044421∼ extracellular region part 1.57E–07 14 Hapln1, Hapln1, Angptl1, Egfl6, Dlk1, Mfap5, Matn1, Col2a1, Hapln1, Epyc, Ptn, Matn3, Hapln1, Matn3, Col9a1, Ccl12, Cxcl14, Comp
UP_SEQ_FEATURE signal peptide 7.64E–07 24 Egfl6, Mia1, Sfrp4, Ccl6, Col2a1, Snorc, Dlk1, Ptn, Matn3, Ecrg4, Matn3, Ccl12, Comp, C1qtnf3, Cd300ld, Angptl1, Nts, Mfap5, Matn1, Cpa3, Epyc, Ecrg4, Mmrn1, Cma1, Col9a1, Cxcl14
UP_SEQ_FEATURE disufide bond 1.86E–06 21 Egfl6, Hapln1, Mia1, Sfrp4, Ccl6, Lect1, Dlk1, Ptn, Matn3, Matn3, Hapln1, Ccl12, Comp, Agtr2, Cd300ld, Angptl1, Hapln1, Matn1, Cpa3, Hapln1, Epyc, Mmrn1, Cma1, Col9a1, Cxcl14
Annotation cluster 2, Enrichment score 3.78
GO: 0005578∼ proteinaceous ECM 1.48E–07 10 Egfl6, Hapln1, Hapln1, Mfap5, Matn1, Col2a1, Hapln1, Epyc, Ptn, Matn3, Matn4, Hapln1, Col9a1, Comp
GO: 0031012∼ extracellular matrix 2.07E–07 10 Egfl6, Hapln1, Hapln1, Mfap5, Matn1, Col2a1, Hapln1, Epyc, Ptn, Matn3, Matn4, Hapln1, Col9a1, Comp
SP_PIR_KEYWORDS extracellular matrix 1.48E–05 7 Hapln1, Hapln1, Egfl6, Hapln1, Mfap5, Col9a1, Comp, Col2a1, Hapln1, Epyc
GO: 0007155∼ cell adhesion 7.13E–03 6 Hapln1, Hapln1, Egfl6, Mia1, Hapln1, Col9a1, Comp, Col2a1, Hapln1
GO: 0022610∼ biological adhesion 7.19E–03 6 Hapln1, Hapln1, Egfl6, Mia1, Hapln1, Col9a1, Comp, Col2a1, Hapln1
Annotation cluster 3, Enrichment score 2.24
SP_PIR_KEYWORDS egf-like domain 2.32E–04 6 Egfl6, Matn3, Mmrn1, Comp, Matn1, Dlk1, Matn3

Annotation cluster analysis of probe sets detecting a significant fold change greater than −2 from wild type to Arhgap28del produced 10 clusters. The top 3 annotation clusters with the highest enrichment score are listed here. A. The top gene ontology components of the cluster. B. The statistical significance of this grouping where the lower the score the more unlikely this clustering is due to chance. C. The number of probe sets that recognize genes contributing to the GO term. D. List of gene names of the Affymetrix Mouse Genome 430 2.0 array probe IDs.