Dysbiosis of skin microbiome and gut microbiome in melanoma progression/Experiment 3
From BugSigDB
Needs review
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
- Cutaneous melanoma cutaneous (skin) melanoma,cutaneous melanoma,cutaneous melanoma (disease),malignant cutaneous melanoma,malignant ear melanoma,malignant lip melanoma,malignant lower limb melanoma,malignant melanoma (of skin), stage unspecified,malignant melanoma of ear and/or external auricular canal,malignant melanoma of skin,malignant melanoma of skin of lower limb,malignant melanoma of skin of trunk except scrotum,malignant melanoma of skin of upper limb,malignant melanoma of skin stage unspecified,malignant neck melanoma,malignant scalp melanoma,malignant trunk melanoma,malignant upper limb melanoma,melanoma (disease) of zone of skin,melanoma of skin,melanoma of the skin,skin melanoma,skin, melanoma,zone of skin melanoma,zone of skin melanoma (disease),Cutaneous melanoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy skin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- melanoma surface from black pigs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cutaneous melanoma surface samples collected from the skin of black pigs
- 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
- 24
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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Supplementary figure 5
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface
Abundance in Group 1: increased abundance in melanoma surface from black pigs
Revision editor(s): Idiaru angela
Signature 2
Needs review
Source: Supplementary figure 5
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface.
Abundance in Group 1: decreased abundance in melanoma surface from black pigs
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Helcococcus | ||
| Moraxella | ||
| Peptoniphilus | ||
| Peptostreptococcus | ||
| Staphylococcus | ||
| Streptococcus | ||
| Escherichia/Shigella sp. |
Revision editor(s): Idiaru angela
