Tumor microbiome diversity influences papillary thyroid cancer invasion/Experiment 1
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
- Thyroid gland Glandula thyroidea,Thyroid,Thyroid gland,thyroid gland
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Papillary thyroid carcinoma papillary cancer of the thyroid,papillary cancer of the thyroid gland,papillary cancer of thyroid,papillary cancer of thyroid gland,papillary carcinoma of the thyroid,papillary carcinoma of the thyroid gland,papillary carcinoma of thyroid,papillary carcinoma of thyroid gland,papillary thyroid cancer,papillary thyroid carcinoma,papillary thyroid gland carcinoma,thyroid gland papillary cancer,thyroid gland papillary carcinoma,thyroid papillary carcinoma,Papillary thyroid carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PTC patients with mild lesions (T1_2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PTC patients with advanced lesions (T3_4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Papillary thyroid cancer (PTC) patients with advanced lesions.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
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).
- arcsine square-root
- 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
- 3.2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2g and 2h
Description: Taxonomic cladogram from LEfSe, depicting taxonomic associations between microbiome communities from patients with T1_2 and T3_4 PTC and LDA score computed from differentially abundant features between T1_2 and T3_4.
Abundance in Group 1: increased abundance in PTC patients with advanced lesions (T3_4)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillales | ||
| Pasteurellales | ||
| Pasteurellaceae | ||
| Hyphomicrobiales | ||
| Streptococcaceae | ||
| Streptococcus | ||
| v2072-189E03v2072-189E03 | ||
| Coriobacteriales | ||
| Granulicatella | ||
| Haemophilus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2g and 2h
Description: Taxonomic cladogram from LEfSe, depicting taxonomic associations between microbiome communities from patients with T1_2 and T3_4 PTC and LDA score computed from differentially abundant features between T1_2 and T3_4.
Abundance in Group 1: decreased abundance in PTC patients with advanced lesions (T3_4)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadaceae | ||
| Pseudomonas | ||
| Pseudomonadales | ||
| Mycobacteriales | ||
| Nocardiaceae | ||
| Rhodococcus | ||
| Sphingomonadales | ||
| Sphingomonadaceae | ||
| Sphingomonas |
Revision editor(s): Aleru Divine
