Nucleolar Database

Nucleolar Proteome Database v 2.0

Database

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The Nucleolar Proteome Database (NoPdb) is a relational database that archives data on more than 700 human proteins identified by multiple mass spectrometry (MS) analyses in the human nucleolus, the most prominent organelle within the nucleus. Each entry is annotated with information about its encoding gene, its protein domain structures and its protein homologues across species, as well as its MS identification history and the corresponding peptides sequenced in tandem MS/MS. The database also provides a gateway to other databases (e.g. LocusLink, OMIM and PubMed).

The database is searchable by gene names, amino acid or nucleotide sequences, sequence motifs, or by limiting the range for isoelectric points and/or molecular weights. The database is also searchable by Interpro motif numbers (database of protein families, domains and functional sites) and by Gene Onotology terms (describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner).

Distribution of proteins in the nucleolar database:

Table 1: Top 10 amino acid motifs found in the nucleolar proteome (referenced to Interpro Database)
(click on IPR number to view all nucleolar proteins which contain the motif)

Interpro ID	Motif Name	Occurrence	Odd ratio	P value*
IPR000504	RNA-binding region RNP-1 (RNA recognition motif)	49	8.68	p<0.001
IPR001650	Helicase, C-terminal	39	17.17	p<0.001
IPR001410	DEAD/DEAH box helicase	39	16.83	p<0.001
IPR001680	G-protein beta WD-40 repeat	36	4.65	p<0.001
IPR008938	ARM repeat fold	24	2.75	p<0.001
IPR007124	Histone-fold/TFIID-TAF/NF-Y	15	11.80	p<0.001
IPR000629	ATP-dependent helicase, DEAD-box	14	34.33	p<0.001
IPR009072	Histone-fold	13	7.61	p<0.001
IPR007125	Histone core	12	13.84	p<0.001
IPR003593	AAA ATPase	9	2.63	p<0.01

The InterPro website can be searched by the IPR numbers listed above to learn more about that particular motif.

*If the frequency of any cell was less than 5, a Fisher exact test was employed showing a two P-tail value; otherwise, a chi-square test with Yates' correction value was employed to calculate the p-value.

Table 2: Top Gene Ontology terms found in the nucleolar proteome (referenced to the Gene Ontology project)
(click on GO number to view all nucleolar proteins which have this gene annotation)

GO term	Description	Occurrence	Odd ratio	P value*
GO:0003723	RNA binding	101	3.70	p<0.001
GO:0006412	protein biosynthesis	60	2.01	p<0.001
GO:0003735	structural constituent of ribosome	50	2.49	p<0.001
GO:0005840	ribosome	42	4.13	p<0.001
GO:0008026	ATP-dependent helicase activity	24	4.92	p<0.001
GO:0006364	rRNA processing	22	18.88	p<0.001
GO:0008380	RNA splicing	21	11.98	p<0.001
GO:0008380	chromosome organization and biogenesis (sensu Eukarya)	21	4.34	p<0.001
GO:0000398	nuclear mRNA splicing, via spliceosome	21	2.65	p<0.001
GO:0006334	nucleosome assembly	20	5.36	p<0.001
GO:0000786	nucleosome	19	5.44	p<0.001
GO:0005694	chromosome	18	4.40	p<0.001
GO:0005730	nucleolus	18	4.26	p<0.001
GO:0008248	pre-mRNA splicing factor activity	18	2.35	p<0.001

To learn more about the Gene Ontology project visit the Gene Ontology website.
More information about the GO annotation can be found on the related AmiGO website.

*If the frequency of any cell was less than 5, a Fisher exact test was employed showing a two P-tail value; otherwise, a chi-square test with Yates' correction value was employed to calculate the p-value.