Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation/Experiment 1
Curated date: 2023/03/14
Curator: BLESSING123
Revision editor(s): WikiWorks, Chloe, BLESSING123, Ifeanyisam
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Survival time survival,time of survival,Survival time,survival time
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Long-term survivors
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Short-term surviviors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cervical Cancer patients that had a follow-up of one year or less because of death
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Signature 1
Source: Figure 2a
Description: The different abundance of bacterial taxa between the two groups were identified by LEfSe. It was significantly different when alpha value of the factorial Kruskal–Wallis test was <0.05 and the logarithmic LDA score was >3.5. The left histogram showed the LDA scores of taxa differentially abundant between the two groups. The taxonomy was listed, followed by its core group. Putative species (Specific OTUs) identified as significantly more enriched/depleted (Fisher/Wilcoxon test p value < 0.05) in patients with short-term vs longterm in baseline samples
Abundance in Group 1: increased abundance in Short-term surviviors
Revision editor(s): BLESSING123, Chloe, WikiWorks
Signature 2
Source: Figure 2a
Description: The different abundance of bacterial taxa between the two groups were identified by LEfSe. It was significantly different when alpha value of the factorial Kruskal–Wallis test was <0.05 and the logarithmic LDA score was >3.5. The left histogram showed the LDA scores of taxa differentially abundant between the two groups. The taxonomy was listed, followed by its core group. Putative species (Specific OTUs) identified as significantly more enriched/depleted (Fisher/Wilcoxon test p value < 0.05) in patients with short-term vs longterm in baseline samples
Abundance in Group 1: decreased abundance in Short-term surviviors
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Porphyromonadaceae | ||
| Porphyromonas |
Revision editor(s): BLESSING123, Chloe, WikiWorks
