Dysbiosis of skin microbiome and gut microbiome in melanoma progression/Experiment 1
Subjects
- Location of subjects
- Czechia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Sus scrofa domesticus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body,skin of body
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Disease staging disease_staging,Disease staging,disease staging
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Melanoma surface of pigs with with melanoma regression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Melanoma surface of pigs with Melanoma progression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Melanoma surface samples collected from piglets with melanoma progression
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
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
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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4A
Description: Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression
Abundance in Group 1: increased abundance in Melanoma surface of pigs with Melanoma progression
Revision editor(s): Snehhumann, Idiaru angela
Signature 2
Source: Figure 4A
Description: Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression
Abundance in Group 1: decreased abundance in Melanoma surface of pigs with Melanoma progression
Revision editor(s): Snehhumann, Idiaru angela
