Table 2.
Available omics resources useful for the study of the helminth intestine.
| Dataset type | Dataset description | Use for intestinal studies |
|---|---|---|
| Genomic | Genome assembly/annotation for A. suum (Jex et al., 2011), H. contortus (Laing et al., 2013), and T. suis (Wang et al., 2015) | Source for all gene and protein sequence information for core helminth intestine species |
| Ortholog matches to other species (Rosa et al., 2014; Wang et al., 2015) |
Gene conservation across helminth species/helminth-specific genes | |
| Wellcome Sanger Institute genome resource (www.sanger.ac.uk/resources/downloads/helminths) | Additional helminth genomes and BLAST database | |
| Wormbase Parasite (https://parasite.wormbase.org) (Howe et al., 2017) |
Helminth genome repository/BLAST services, gene enrichment testing/variant effect predictor | |
| Genomic functional annotations | KEGG (Kanehisa et al., 2016) |
Biological pathways relevant to intestine |
| Gene ontology (Ashburner et al., 2000) |
GO terms related to intestine | |
| MEROPS (peptidases) (Rawlings and Morton, 2008) |
Specific classification of digestive peptidases | |
| Interpro domains (Hunter et al., 2012; Jones et al., 2014) |
Additional specific functional annotation | |
| 5’ upstream UTR binding motifs (Rosa et al., 2014) |
Identify transcription factors that may modulate expression of intestinal genes | |
| RNAi phenotype in C. elegans
(Piano et al., 2000; Piano et al., 2002; Fernandez et al., 2005; Sönnichsen et al., 2005) |
Identify intestine-related and lethal/sterile phenotypes | |
| Protein–protein interactions* (Simonis et al., 2009) |
Target intestinal proteins that interact with many other intestinal proteins | |
| Transcriptomic | RNA-Seq of 10 A. suum tissues (Rosa et al., 2014) |
Identify intestine-overexpressed genes in adult male and female A. suum |
| RNA-Seq of anterior, middle and posterior A. suum intestine (Gao et al., 2016) | Identify intestinal genes and miRNAs expressed more highly in various regions of the intestine | |
| Intestinal RNA-Seq expression from H. contortus and T. suis (Wang et al., 2015) | Identify intestine-expressed genes in phylogenetically distinct A. suum orthologs | |
| Proteomic | Proteins detected in various A. suum intestinal compartments (Rosa et al., 2015) |
Confident identification of proteins from intestinal tissue, apical and peripheral intestinal membranes, intestinal lumen, and pseudocoelomic fluid |
| Peptidases in A. suum intestine (Jasmer et al., 2015) |
Detailed list of proteomics-confirmed peptidases on the apical intestinal membrane, and in the intestinal lumen | |
| Multiomics | Intestinal families (IntFams) (Wang et al., 2015) |
Confident nematode-conserved and consistently intestine-expressed genes using multiple species |
| Helminth.net online resource (Martin et al., 2015) |
A collection of omics databases with tools to search genes and functions, perform BLAST searches, view KEGG pathways, browse variants, and perform multiomics comparisons to identify drug and vaccine targets |
*Inferred using the closest significant C. elegans ortholog.