Additional file 11: Figure S1. of A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions

The number of sequences categorized by their source organisms. (PDF 837 kb

The enrichment analysis page.

<p>EnHERV’s enrichment analysis page. EnHERV gives the Fisher’s exact, P-value and odd ratio of the designed enrichment analysis. EnHERV also provides parallel analysis for sub-selected HERV superfamily/family.</p

HERV truncation pattern distribution.

<p>Percentage and number of each HERV truncation pattern in the HERV elements resulting from the defragmentation process.</p

The number of defragmented elements, resulting from HERV defragmentation using REannotate with different values of distance parameters, and their coverage percentages.

<p>The number of defragmented elements, resulting from HERV defragmentation using REannotate with different values of distance parameters, and their coverage percentages.</p

Solo LTRs used in the enrichment analysis in EnHERV.

<p>Solo LTRs used in the enrichment analysis in EnHERV.</p

HERV superfamily distribution.

<p>Percentage and number of copy of each HERV superfamily in hg19/GRCh37 genome. 687,420 HERV elements were distributed into 5 groups including 4 superfamilies and one unclassified group. Almost 50% of HERV elements in the human genome belongs to the ERVL-MaLR superfamily.</p

Number of defragmented and non-defragmented elements.

<p>Graph shows a number of defragmented and non-defragmented elements in relation to distance parameters.</p

<i>ETS1</i> Haplotype analysis on SLE association.

<p><i>ETS1</i> Haplotype analysis on SLE association.</p

Confirmation of association of <i>HLA</i> locus, and <i>TNFSF4</i>, <i>STAT4</i>, <i>TNFAIP3</i>, <i>IRF5</i>, <i>BLK</i> with SLE.

<p>Shown are association results comparing SLE patients with controls collected in Hong Kong analyzed by Plink (−log₁₀(<i>P</i>-value) of SNPs). The best SNP in Chromosome 11 is around <i>ETS1</i> gene (rs6590330), which is in high LD with rs1128334. And the best SNP in Chromosome 10 is in <i>WDFY4</i> (rs877819).</p

Replication of disease association for <i>WDFY4</i> SNPs in the Hong Kong samples.

<p>Replication of disease association for <i>WDFY4</i> SNPs in the Hong Kong samples.</p