Pronounced gut microbiota signatures in patients with JAK2V617F-positive essential thrombocythemia/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-5-31
Subjects
- Location of subjects
- Denmark
- 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
- Essential thrombocythemia essential thrombocytemia,essential thrombocythaemia,essential thrombocythemia,essential thrombocytosis,ET,hemorrhagic thrombocythemia,idiopathic thrombocythemia,primary thrombocythemia,primary thrombocytosis,Essential thrombocythemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Essential thrombocythemia (ET)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with essential thrombocythemia (ET), a cancer characterized by thrombocyte overproduction
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 54
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 0.005
- Matched on Factors on which subjects have been matched on in a case-control study
- sex
Alpha Diversity
- 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
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-5-31
Source: Fig 6a
Description: Differential abundance analysis identified using LEfSe between healthy controls and patients with Essential Thrombocythemia
Abundance in Group 1: increased abundance in Essential thrombocythemia (ET)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Coriobacteriales | ||
| Coriobacteriia | ||
| Erysipelotrichaceae | ||
| Veillonella |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-5-31
Source: Fig 6a
Description: Differential abundance analysis identified using LEfSe between healthy controls and patients with Essential Thrombocythemia
Abundance in Group 1: decreased abundance in Essential thrombocythemia (ET)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Clostridia | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Lachnospiraceae | ||
| Lachnospirales | ||
| Oscillospiraceae | ||
| Bacillota |
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