Dysbiosis of skin microbiome and gut microbiome in melanoma progression/Experiment 5
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Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
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
- 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
- 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
- controls without melanoma and melanoma regression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Melanoma progression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples collected from piglets undergoing melanoma progression.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 7
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples
Abundance in Group 1: increased abundance in Melanoma progression
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Filifactor | ||
| Fusobacterium | ||
| Helcococcus | ||
| Odoribacter | ||
| Faecalibacterium sp. UBA1819 |
Revision editor(s): Idiaru angela, WikiWorks
