32488167/Experiment 1: Difference between revisions
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|16S variable region (lower bound)=4 | |16S variable region (lower bound)=4 | ||
|Sequencing platform=Illumina | |Sequencing platform=Illumina | ||
|Data transformation=relative abundances | |||
|Statistical test=Kruskall-Wallis | |Statistical test=Kruskall-Wallis | ||
|Significance threshold=0.05 | |Significance threshold=0.05 | ||
Revision as of 19:31, 2 November 2023
Curated date: 2021/10/28
Curator: Joyessa
Revision editor(s): WikiWorks, Claregrieve1, Joyessa, Peace Sandy
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 Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gestational age Gestational age,gestational age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Week 24
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Week 36
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gestational age of 36 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 56
- Group 1 sample size Number of subjects in the case (exposed) group
- 57
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).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Curated date: 2021/10/28
Curator: Joyessa
Revision editor(s): WikiWorks, Fatima, Claregrieve1, Joyessa
Source: Figure 3
Description: Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.
Abundance in Group 1: increased abundance in Week 36
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella | ||
| Streptococcus | ||
| Staphylococcus | ||
| Enterococcus | ||
| Corynebacterium | ||
| Gemella |
Revision editor(s): WikiWorks, Fatima, Claregrieve1, Joyessa
Signature 2
Curated date: 2021/10/28
Curator: Joyessa
Revision editor(s): WikiWorks, Fatima, Claregrieve1, Joyessa
Source: Figure 3
Description: Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.
Abundance in Group 1: increased abundance in Week 36
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): WikiWorks, Fatima, Claregrieve1, Joyessa
