Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB

Abstract

Precocious puberty (PP) is an important endocrine disorder affecting children globally. Several genes, SNPs and comorbidities are reported to be associated with PP; however, this data is scattered across scientific literature and has not been systematically collated and analysed. In this study, we present PrecocityDB as the first manually curated online database on genes and their ontology terms, SNPs, and pathways associated with PP. A tool for visualizing SNP coordinates and allelic variation on each chromosome, for genes associated with PP is also incorporated in PrecocityDB. Pathway enrichment analysis of PP-associated genes revealed that endocrine and cancer-related pathways are highly enriched. Disease enrichment analysis indicated that individuals with PP seem to be highly likely to suffer from reproductive and metabolic disorders such as PCOS, hypogonadism, and insulin resistance. PrecocityDB is a useful resource for identification of comorbid conditions and disease risks due to shared genes in PP. PrecocityDB is freely accessible at http://www.precocity.bicnirrh.res.in. The database source code and content can be downloaded through GitHub (https://github.com/bic-nirrh/precocity).

EPEK: creation and analysis of an Ectopic Pregnancy Expression Knowledgebase

“…Therefore, we were motivated to check for resources specific to other maternal health disorders that might have captured the genes associated with EP. We identified curated resources like PrecocityDB [10] associated with precocious puberty, PCOSKB [11] associated with polycystic ovary syndrome, Endometriosis Knowledgebase [12] associated with endometriosis, and CCDB [13] associated with cervical cancer. Further, Barbitoff et al .…”

“…Knowledgebases built on comparative studies are helpful in deciphering the underlying pathophysiology of various human diseases. In particular, different 4 knowledgebases built for maternal health disorders relied on the differential expression of genes or proteins [10][11][12][13]. Such data-driven knowledgebases have highlighted the molecular mechanisms implicated in these diseases.…”

EPEK: Creation and analysis of an Ectopic Pregnancy Expression Knowledgebase

“…The copyright holder for this preprint this version posted December 20, 2022. ; https://doi.org/10.1101/2022.12.20.521279 doi: bioRxiv preprint to check for resources specific to other maternal health disorders that might have captured the genes associated with EP. We identified curated resources like PrecocityDB [10] associated with precocious puberty, PCOSKB [11] associated with polycystic ovary syndrome, Endometriosis Knowledgebase [12] associated with endometriosis, and CCDB [13] associated with cervical cancer. Further, Barbitoff et al [56] have manually curated the list of genes associated with 4 common pregnancy complications namely, preeclampsia, gestational diabetes, placental abruption and preterm birth from public resources.…”

“…The copyright holder for this preprint this version posted December 20, 2022. ; https://doi.org/10.1101/2022.12.20.521279 doi: bioRxiv preprint 4 knowledgebases built for maternal health disorders relied on the differential expression of genes or proteins [10][11][12][13]. Such data-driven knowledgebases have highlighted the molecular mechanisms implicated in these diseases.…”