Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women/Experiment 7
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical glandular intraepithelial neoplasia Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high grade dysplasia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high grade dysplasia confirmed by histology of colonoscopy-directed biopsy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, ethnic group
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Figure 4
Description: Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity
Abundance in Group 1: increased abundance in high grade dysplasia
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Gardnerella | ||
| Lactobacillus iners | ||
| Megasphaera | ||
| Parvimonas | ||
| Prevotella amnii | ||
| Shuttleworthella | ||
| Sneathia | ||
| Sneathia sanguinegens |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Curated date: 2021/01/10
Curator: Cynthia Anderson
Revision editor(s): Fatima, WikiWorks, ChiomaBlessing
Source: Figure 4
Description: Enrichment in bacterial taxa in the high grade dysplasia group when compared to HPV-negative control after adjusting for age, BMI and ethnicity
Abundance in Group 1: decreased abundance in high grade dysplasia
Revision editor(s): Fatima, WikiWorks, ChiomaBlessing
