Metagenome-assembled microbial genomes from Parkinson's disease fecal samples/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Subjects
- Location of subjects
- Finland
- 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
- Parkinson's disease IDIOPATHIC PARKINSON DIS,Idiopathic Parkinson Disease,Idiopathic Parkinson's Disease,IDIOPATHIC PARKINSONS DIS,Idiopathic PD,LEWY BODY PARKINSON DIS,Lewy Body Parkinson Disease,Lewy Body Parkinson's Disease,Paralysis agitans,paralysis agitans,PARKINSON DIS,PARKINSON DIS IDIOPATHIC,Parkinson disease,Parkinson Disease, Idiopathic,Parkinson syndrome,Parkinson's,Parkinson's disease,Parkinson's disease (disorder),Parkinson's disease NOS,Parkinson's disease NOS (disorder),Parkinson's Disease, Idiopathic,Parkinson's Disease, Lewy Body,Parkinson's syndrome,Parkinsonian disorder,Parkinsonism, Primary,Parkinsons,PARKINSONS DIS,PARKINSONS DIS IDIOPATHIC,PARKINSONS DIS LEWY BODY,Parkinsons disease,Primary Parkinsonism,parkinson's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson’s disease (PD) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients refers to patients diagnosed of Parkinson’s disease (PD) - a common neurodegenerative disease.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 68
- Group 1 sample size Number of subjects in the case (exposed) group
- 68
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Source: Supplementary Table 14
Description: Differential abundance of taxa between Control and PD patients using DESeq2
Abundance in Group 1: increased abundance in Parkinson’s disease (PD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobrevibacter smithii | ||
| Methanomethylophilus alvi |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-4
Source: Supplementary Table 14
Description: Differential abundance of taxa between Control and PD patients using DESeq2
Abundance in Group 1: decreased abundance in Parkinson’s disease (PD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Methanomethylophilaceae UBA71Methanomethylophilaceae UBA71 | ||
| Candidatus Methanomassiliicoccus intestinalis |
Revision editor(s): KateRasheed
