The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2023-2-26
Subjects
- Location of subjects
- China
- 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
- Uterus Uterus,uterus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Ovarian cancer cancer of ovary,cancer of the ovary,malignant neoplasm of ovary,malignant neoplasm of the ovary,malignant ovarian neoplasm,malignant ovarian tumor,malignant ovary neoplasm,malignant tumor of ovary,malignant tumor of the ovary,malignant tumour of ovary,ovarian cancer,ovarian cancer, epithelial,ovarian malignant tumor,ovarian neoplasm,ovary cancer,ovary neoplasm,primary ovarian cancer,tumor of the ovary,Ovarian cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ovarian cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- preliminary diagnosis of suspected ovarian cancer and undergoing laparotomy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/12/23
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): Lwaldron, WikiWorks, LGeistlinger
Source: Figure 3, Table 2
Description: Differential relative abundance of taxa in ovarian communities between patients in cancer an control group.
Abundance in Group 1: increased abundance in ovarian cancer
Revision editor(s): Lwaldron, WikiWorks, LGeistlinger
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/12/23
Source: Figure 3, Table 2
Description: Differential relative abundance of taxa in ovarian communities between patients in cancer an control group
Abundance in Group 1: decreased abundance in ovarian cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Thermoproteota | ||
| Sphingobacteriia | ||
| Halobacteriales | ||
| Flavobacteriaceae | ||
| Archaeoglobaceae | ||
| Leptotrichiaceae | ||
| Methanocorpusculaceae | ||
| Geodermatophilaceae | ||
| Paenibacillus | ||
| Haloferax |
Revision editor(s): WikiWorks
