Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome

BMC Genomics

Table 3 Gene ontology term enrichment of unique SIDER-associated orthologous Leishmania genes

Gene Ontology term	P-value	Fold enrichment^a	Orthologs
SIDER-associated genes in *L. major* , *L. infantum* , and *L. braziliensis* (439 sampled) ^b
Biological Process
Nitrogen compound biosynthetic process	6.9E-6	3.8×	13
Cofactor metabolic process	4.1E-3	2.1×	14
Methionine metabolic process	9.3E-3	7.0×	3
Molecular Function
Cofactor binding	3.7E-4	2.1×	23
Oxidoreductase activity	7.9E-4	1.6×	46
Acyl-CoA dehydrogenase activity	3.0E-3	4.5×	4
Vitamin binding	3.2E-3	2.3×	13
SIDER-associated genes in *L. major* and *L. infantum* (163 sampled) ^b
Biological Process
Post-translational protein modification	6.5E-3	1.8×	20
Molecular Function
Hydrolase activity, acting on ester bonds	6.9E-3	2.0×	16
Phosphotransferase activity, alcohol group as acceptor	7.3E-3	1.8×	19
Carbon-sulfur lyase activity	8.3E-3	12×	2
Methyltransferase activity	9.3E-3	2.7×	8
SIDER-associated genes in *L. major* and *L. braziliensis* (28 sampled) ^b
n/a
SIDER-associated genes in *L. infantum* and *L. braziliensis* (27 sampled) ^b
n/a
SIDER-associated genes in *L. major* only (94 sampled) ^b
n/a
SIDER-associated genes in *L. infantum* only (47 sampled) ^b
n/a
SIDER-associated genes in *L. braziliensis* only (156 sampled) ^b
Biological Process
Ribonucleoside metabolic process	6.4E-3	6.3×	3
Regulation of mitotic cell cycle	7.6E-3	13×	2
Molecular Function
Aspartic-type endopeptidase activity	6.4E-3	6.3×	3

^a [Sample frequency]/[Background frequency]
^bSampled genes exclude hypothetical proteins with no assigned function.
SIDER-associated orthologs were separated into 7 distinct subgroups for Gene Ontology term enrichment using AmigGO [38]. The unique corresponding L. major orthologs with annotated GO terms in each subgroup were sampled against a background of all functionally annotated genes in L. major. Only P-values ≤ 10^-2 (rmq: most of the values are between 10^-2 and 10^-3) and over 1.5× enrichment are presented. n/a: not applicable.

ISSN: 1471-2164