Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women/Experiment 3

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
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


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 high grade dysplasia group when compared to HPV-negative control prior to adjusting

Abundance in Group 1: increased abundance in high grade dysplasia

NCBI Quality ControlLinks
Atopobium
Clostridium
Fannyhessea vaginae
Gardnerella
Hoylesella buccalis
Megasphaera
Parvimonas
Prevotella amnii
Shuttleworthia
Sneathia
Sneathia sanguinegens
Streptococcus agalactiae

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 high grade dysplasia group when compared to HPV-negative control prior to adjusting

Abundance in Group 1: decreased abundance in high grade dysplasia

NCBI Quality ControlLinks
Anaerococcus lactolyticus
Anaerococcus obesiensis
Bifidobacterium
Dialister
Dialister propionicifaciens
Fenollaria massiliensis
Finegoldia magna
Lactobacillus
Lactobacillus gasseri
Peptoniphilus coxii
Peptoniphilus duerdenii
Peptoniphilus grossensis
Peptoniphilus lacrimalis
Porphyromonas
Prevotella bivia
Prevotella corporis
Prevotella disiens
Streptococcus
Ureaplasma

Revision editor(s): WikiWorks, ChiomaBlessing