Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes

Abstract

Background The nematode worm, Caenorhabditis elegans, is a saprophytic species that has been emerging as a standard model organism since the early 1960s. This species is useful in numerous fields, including developmental biology, neurobiology, and ageing. A high-quality comprehensive molecular interaction network is needed to facilitate molecular mechanism studies in C. elegans. Results We present the predicted functional interactome of Caenorhabditis elegans (FIC), which integrates functional association data from 10 public databases to infer functional gene interactions on diverse functional perspectives. In this work, FIC includes 108,550 putative functional associations with balanced sensitivity and specificity, which are expected to cover 21.42% of all C. elegans protein interactions, and 29.25% of these associations may represent protein interactions. Based on FIC, we developed a gene set linkage analysis (GSLA) web tool to interpret potential functional impacts from a set of differentially expressed genes observed in transcriptome analyses. Conclusion We present the predicted C. elegans interactome database FIC, which is a high-quality database of predicted functional interactions among genes. The functional interactions in FIC serve as a good reference interactome for GSLA to annotate differentially expressed genes for their potential functional impacts. In a case study, the FIC/GSLA system shows more comprehensive and concise annotations compared to other widely used gene set annotation tools, including PANTHER and DAVID. FIC and its associated GSLA are available at the website http://worm.biomedtzc.cn.

New immunological potential markers for triple negative breast cancer: IL18R1, CD53, TRIM, Jaw1, LTB, PTPRCAP

“…Breast cancer is an heterogeneous disease, characterized by histopathological and genetically defined subtypes that make difficult to delineate specific prognostic factors and efficacious therapies [41], as it occurs also in several other tumours [42][43][44]. Indeed, the definition of prognostic markers is a serious issue [45,46] that is a primary research goal for precision oncology [47,48], highlighting the need for novel specific progression and prognostic molecular clusters able to stratify cohort of patients with distinct prognostic outcome [49,50]. One of such markers, identified from the elucidation of novel molecular mechanisms underlying the progression of breast cancer, is the transcription marker p63.…”

Expanding Interactome Analyses beyond Model Eukaryotes

“…C. elegans is a free-living nematode that was one of the first eukaryotes [13] to have its genome sequenced [374], and considerable effort has been put into completing the interactome of this species [375], and in the comparison between its interactome and those of other model eukaryotes [307]. Several computationally-predicted interactomes have also been produced [13,188,198,[376][377][378][379][380][381].…”