Data · dataset · 2023
Protein identity, features and gene expression levels of S. stercoralis orthologues of S. ratti E/S proteomic data
Listed in LSHTM Data Compass
S. ratti E/S proteins (from Hunt et al., 2016) were searched against a custom blast+ database consisting of the S. stercoralis genome-derived proteome (from WBPS v8) to obtain homologues.
Description
E-value -50 and word size 2 were used to perform the search. Protein identities are given for the original S. ratti proteins (from Hunt et al., 2016) and the BLAST KOALA results from this study along with corresponding KEGG orthology.
Gene expression in normalised read count is from analysis of data from different life stages of S. stercoralis (obtained from Stoltzfus et al., (2012)). Overlap is indicated with proteins which were also differentially expressed (DE) with 100% certainty between gut-dwelling and non-gut-dwelling life stages, as determined for this study. Proteins containing predicted epitopes according to two tools: BepiPred 1.0 and bcepred are indicated as well as proteins predicted by SignalP to contain a signal peptide.
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Accession numbers starting ERR refer to RNA-seq data in NCBI SRA and those starting SSTP are S. stercoralis gene transcripts which may be found in UniProt or WormBase ParaSite. Life-stage abbreviations are explained in the manuscript text.
Links
Where it is published
- DOI doi.org/10.1371/journal.pntd.0010777.s004 ↗
DOI / persistent id · from lshtm ac uk
Catalogue records · 1
- OAI-PMH record datacompass.lshtm.ac.uk/cgi/oai2?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3… ↗
metadata API · from lshtm ac uk
Topics
- From keywords
- Earth & Environmental Science · Humanities · Life Sciences · Medicine & Health · Social Science
- Inferred from text
- Genetics 72% · RNA sequencing 65% · Text 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| LSHTM Data Compass | oai:datacompass.lshtm.ac.uk:3406 | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:group:3105 | enrichment · lshtm ac uk | taxonomy-embedding@1.0.0 | title+keywords+description (72%) |
| concepts[field].local:field:earth-environmental | mapping · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · lshtm ac uk | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:text | enrichment · lshtm ac uk | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | /metadata/dc/description |
| publication_date | source · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | |
| title | source · lshtm ac uk | connector:lshtm_ac_uk@1.0.0 | /metadata/dc/title |