Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-7-18
Subjects
- Location of subjects
- India
- 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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral cavity carcinoma carcinoma of mouth,carcinoma of oral cavity,carcinoma of the oral cavity,mouth carcinoma,oral cavity cancer,oral cavity carcinoma,Oral cavity carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adjacent normal tissue (AT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Precancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Precancerous lesion samples were collected from patients with leukoplakia, fibrosis, and erythroplakia.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
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
- 2.0
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-18
Source: Supplementary Figure 2C, 3B and 3D
Description: Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and Precancer Samples.
Abundance in Group 1: decreased abundance in Precancer
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-18
Source: Supplementary Figure 3D
Description: Differential abundances of core bacterial Species among adjacent tumor tissue and Precancer lesions.
Abundance in Group 1: increased abundance in Precancer
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus periodonticum |
