Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

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
Human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,Human papilloma virus infection
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
HPV+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HPV+ determined by the Linear Array HPV Genotyping Tests
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
31
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


Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Figure 4

Description: Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control prior to adjusting

Abundance in Group 1: increased abundance in HPV+

NCBI Quality ControlLinks
Prevotella
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): WikiWorks, ChiomaBlessing

Source: Figure 4

Description: Enrichment in bacterial taxa in the HPV+ group when compared to HPV-negative control prior to adjusting

Abundance in Group 1: decreased abundance in HPV+

NCBI Quality ControlLinks
Actinomyces
Anaerococcus lactolyticus
Bifidobacterium
Dialister
Fenollaria massiliensis
Fusobacterium nucleatum
Gardnerella
Lactobacillus
Lactobacillus gasseri
Mobiluncus mulieris
Peptoniphilus grossensis
Streptococcus anginosus

Revision editor(s): WikiWorks, ChiomaBlessing