Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
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
- Mucosa of oral region Mucosa of oral opening,Mucosa of oral part of face,Mucosa of organ of oral opening,Mucosa of organ of oral part of face,Mucosa of organ of oral region,Mucosa of organ of subdivision of mouth,Mucosa of subdivision of mouth,Mucous membrane of oral opening,Mucous membrane of oral part of face,Mucous membrane of oral region,Mucous membrane of subdivision of mouth,Oral opening mucosa,Oral opening mucosa of organ,Oral opening mucous membrane,Oral opening organ mucosa,Oral part of face mucosa,Oral part of face mucosa of organ,Oral part of face mucous membrane,Oral part of face organ mucosa,Oral region mucosa,Oral region mucosa of organ,Oral region mucous membrane,Oral region organ mucosa,Organ mucosa of oral opening,Organ mucosa of oral part of face,Organ mucosa of oral region,Organ mucosa of subdivision of mouth,Subdivision of mouth mucosa,Subdivision of mouth mucosa of organ,Subdivision of mouth mucous membrane,Subdivision of mouth organ mucosa,Mucosa of oral region,mucosa of oral region
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral squamous cell carcinoma mouth scc,mouth squamous cell carcinoma,OCSC,oral cavity scc,oral cavity squamous cell cancer,oral cavity squamous cell carcinoma,oral squamous cell carcinoma,scc of mouth,scc of oral cavity,scc of the mouth,scc of the oral cavity,squamous cell carcinoma of mouth,squamous cell carcinoma of oral cavity,squamous cell carcinoma of the mouth,squamous cell carcinoma of the oral cavity,Oral squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paracancerous tissues
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous lesions
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients at different stages of OSCC were enrolled in the study
- 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
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
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
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Source: Figure 2A
Description: Relative abundance of genera enriched in cancerous tissues VS paracancerous tissues
Abundance in Group 1: increased abundance in cancerous lesions
| NCBI | Quality Control | Links |
|---|---|---|
| Carnobacterium | ||
| Filifactor | ||
| Fusobacterium | ||
| Parvimonas | ||
| Peptostreptococcus | ||
| Streptococcus | ||
| Tannerella | ||
| Treponema |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-8
Curated date: 2021/01/10
Curator: Rimsha Azhar
Revision editor(s): Atrayees, WikiWorks, ChiomaBlessing
Source: Figure 2A
Description: Relative abundance of genera enriched in cancerous tissues VS paracancerous tissues
Abundance in Group 1: decreased abundance in cancerous lesions
| NCBI | Quality Control | Links |
|---|---|---|
| Arthrobacter | ||
| Brevundimonas | ||
| Desulfovibrio | ||
| Microbacterium | ||
| Mucispirillum | ||
| Paenibacillus | ||
| Streptophyta |
Revision editor(s): Atrayees, WikiWorks, ChiomaBlessing
