Characteristics and clustering of human ribosomal protein genes

BMC Genomics

Table 3 Features of specific RP genes.

RP genes	Features
RPLP0	Unique gene expression profile was observed. Amino acid composition was unique.
RPLP1, RPLP2	They were highly expressed in LND and keratinocytes. The frequencies of lysine and arginine were low.
RPL41	The size was shortest. Amino acid composition was unique. The level of GC₃ was lowest, and codon composition was unique.
RPSA	The frequencies of lysine and arginine were low. Codon composition was unique.
RPS6	Codon composition was unique.
RPS18	It was highly expressed in bone marrow and stomach.
RPS26	It was highly expressed in small intestine, adipose mesangium and liver. The frequency of lysine was low.
RPS27	The frequencies of lysine and arginine were low.
RPS29	The frequency of lysine was low. Codon composition was unique.
RPL5	Codon composition was unique.
RPL14	The frequency of arginine was low. Trinucleotide (GCT) repeats was contained.
RPL28	It was highly expressed in osteoblast. Codon composition was unique.
RPL36A	The frequency of cysteine was high.

The feature index (FI) is a quantitative measure of the heterogeneity in an individual RP gene. Expression profile, amino acids encoded, and synonymous codon composition: a value of 1 was given to genes that did not belong to the Main cluster. TATA box: a value of 1 was given to genes that had TATA boxes. Common promoter: the maximum value was set as 0.4, because no obvious clusters were found for the analysis of promoter prediction. Then, if a binding site for one of four common transcription factors (nuclear respiratory factor 2 (NRF), GC boxes (GC), Yin and Yang 1 (YY), and activator protein 1 (AP)) was found, a value of 0.1 was subtracted. The columns "Expression profile cluster", "Amino acid encoding cluster", and "Synonymous codon frequency cluster" indicate the clusters to which RP genes were assigned as a result of each analysis. M: Main cluster; S1: Sub-cluster 1; S2: Sub-cluster 2; O: Other. The column "TATA box" indicates the existence of a TATA box, Y: Yes, N: No. For example, FI 3.3 of RPLP0 was calculated as follows; +1.0 (Expression profile), +1.0 (Amino acid encoding cluster), +0 (Synonymous codon frequency), +1.0 (TATA box), +0.4 -0.1 (Predicted Transcription Factors bound).

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