SUS-BAR

Statistics

The following tables show statistical information about the SUS-BAR database.

In Table 1 the total number of pig proteins, as retrieved from the present releases of the databases, is sorted out based on the number of sequences endowed with unique Gene Ontology of the three main roots (Molecular Function (MF); Biological Process (BP); Cellular Component (CC)), with all the GO terms (All-GO), with Pfam domains (Pfam), with both Pfam and All-GO (Pfam & All-GO) terms and with a structure in the Protein database (PDB). Sequences are also listed depending on the UniProtKB branch from where there were retrieved (SwissProt, manually annotated and reviewed, and TrEMBL, automatically annotated).

Table 1. Annotation of the PIG proteome in UniProtKB and Ensembl

		MF	BP	CC	All-GO	Pfam°	Pfam &All-GO	PDB*
SwissProt ^[1,406]	Sequences	1,159	966	1,259	1,377	1,288	1,392	112
SwissProt ^[1,406]	Terms	765	1,234	262	2,261	961	3,222	-
TrEMBL ^[18,170]	Sequences	9,514	4,556	5,817	11,230	13,092	14,934	0
TrEMBL ^[18,170]	Terms	895	983	247	2,125	3,712	5,837	-
Ensembl ^[15,805]	Sequences	12,369	11,295	10,500	13,583	12,981	13,832	77
Ensembl ^[15,805]	Terms	2,632	6,867	947	10,446	4,150	14,596	-
Total ^[35,381]	Sequences	23,042	16,817	17,576	26,190	27,361	30,158	189
Total ^[35,381]	Terms	2,657	6,890	949	10,496	4,324	14,820	-

With our method all the pig protein sequences are aligned towards the BAR+ database and they may enter into a cluster containing statistically validated information (P value<0.01) for a specific GO term or Pfam domain. This is the case for 26,320 pig protein sequences while 9,061 remain singletons and carry along the UniProtKB or Ensembl annotation (when present). 83% of the cluster-retained sequences align towards clusters endowed with statistically validated annotation and they inherit all the cluster statistically validated GO terms and/or Pfam domains. In Table 2, with the symbol ° we identify terms that are statistically validated and have an experimental evidence code.

Table 2. Statistically validated annotation of the PIG proteome in SUS-BAR

		MF	MF°	BP	BP°	CC	CC°	All-GO	All-GO°	Pfam	Pfam & All-GO	*PDB
Cluster ^[26,320]	Sequences	17,152	12,380	16,567	13,359	16,571	13,187	19,820	15,785	20,690	21,793	9,383
	Clusters	6,929	3,973	6,482	4,599	6,442	4,497	8,578	5,974	9,212	9,941	3,528
	Terms	3,668	3,069	10,325	9,896	1,369	1,234	15,362	14,199	3,941	19,303	-
^§Singleton ^[9,061]	Sequences	4,596	11	3,095	8	3,084	10	5,280	16	5,697	6,406	30
^§Singleton ^[9,061]	Terms	1,090	33	2,966	184	552	43	4,608	260	2,058	6,666	-
Total ^[35,381]	Sequences	21,748	12,391	19,662	13,367	19,655	13,197	25,100	15,801	26,387	28,199	9,413
Total ^[35,381]	Terms	3,730	3,070	10,533	9,900	1,393	1,235	15,656	14,205	4,220	19,876	-

In Table 3 the effect of our annotation procedure is shown for sequences without any annotation in UniProtKB and Ensembl.

Table 3. SUS-BAR annotation of pig protein sequences not annotated in UniProtKB and Ensembl

		MF	BP	CC	All-GO	Pfam	Pfam & All-GO	*PDB
UniProtKB ^[3,250]	Sequences	285	418	456	607	234	666	124
	Clusters	240	358	396	526	204	580	101
	Terms	515	2,232	426	3,173	154	3,327	-
Ensembl ^[2,370]	Sequences	90	104	131	175	77	202	31
	Clusters	73	83	104	142	58	159	23
	Terms	189	656	262	1,107	65	1,172	-
Total ^[5,620]	Sequences	375	522	587	782	311	868	155
	Clusters	282	402	453	607	247	674	113
	Terms	545	2,311	467	3,323	195	3,518	-

In Table 4 the search by Homo sapiens, Mus musculus and Bos taurus retrieves all the clusters where sequences of the three organisms share some annotation with those of the pig animal, including, when available, a structural template. Interestingly a large fraction of the pig protein sequences inherit from the clusters statistically validated annotation albeit the low sequence identity (SI< 30%) with sequences carrying information into the cluster.

Table 4. PIG sequences in clusters with other organisms

Organism	#Clusters	#Pig Sequences	#Pig Sequences (SI<30%)	#Clusters with PDB	#Pig Sequences inheriting PDBs
Homo sapiens	10,475	22,581	3,958	3,487	9,314
Mus musculus	9,778	21,648	4,525	3,430	9,222
Bos taurus	9,303	21,044	4,238	3,305	9,050