Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Subjects
- Location of subjects
- China
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sjogren syndrome Mikulicz disease,primary Sjogren-Gougerot syndrome,primary Sjögren syndrome,primary Sjögren-Gougerot syndrome,Sicca (Sjogren's) syndrome,Sicca syndrome,sicca syndrome,Sicca syndrome (disorder),Sjgren's syndrome (disorder),Sjogren syndrome,Sjogren's disease,SJOGREN'S SYNDROME,Sjogren's syndrome,Sjogren's syndrome (disorder),Sjogrens Syndrome,Sjögren syndrome,Syndrome, Sicca,Syndrome, Sjogren's,syndrome, Sjogren's,xerodermosteosis,sjogren's syndrome,sjogren syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PSS
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Sjogren syndrome
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 3
Description: Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls
Abundance in Group 1: increased abundance in PSS
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Selenomonadales | ||
| Veillonellaceae | ||
| Gammaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 3
Description: Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls
Abundance in Group 1: decreased abundance in PSS
Revision editor(s): WikiWorks
