Tumor microbiome diversity influences papillary thyroid cancer invasion
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with PTC at clinical stage T1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with PTC at clinical stage T2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Papillary thyroid cancer (PTC) at clinical stage T2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
Statistical Analysis
- Statistical test
- Welch's T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with PTC at clinical stage T3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Papillary thyroid cancer (PTC) at clinical stage T3.
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2f
Description: Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.
Abundance in Group 1: decreased abundance in Patients with PTC at clinical stage T3
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas | ||
| Rhodococcus | ||
| Sphingomonas |
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with PTC at clinical stage T4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Papillary thyroid cancer (PTC) at clinical stage T4.
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2f
Description: Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.
Abundance in Group 1: decreased abundance in Patients with PTC at clinical stage T4
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with PTC at clinical stage T2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with PTC at clinical stage T3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Papillary thyroid cancer (PTC) at clinical stage T3.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2f
Description: Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.
Abundance in Group 1: decreased abundance in Patients with PTC at clinical stage T3
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas | ||
| Sphingomonas |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with PTC at clinical stage T4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Papillary thyroid cancer (PTC) at clinical stage T4.
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2f
Description: Microbiome alterations at the genus level in patients with PTC of clinical stages T1–T4. Intragroup differences were analyzed using the Kruskal–Wallis test, and differences between groups were analyzed based on the post-hoc test using Welch’s uncorrected test, adjusted by false discovery rate. The top three differential bacteria (genus) identified were tested individually.
Abundance in Group 1: decreased abundance in Patients with PTC at clinical stage T4
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with PTC at clinical stage T3
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male Patients with PTC (G1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female Patients with PTC (G2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female Patients with Papillary thyroid cancer (PTC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
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 4c
Description: Microbiome alterations at the genus level in patients of different sexes with PTC. Differences between groups were analyzed using the Wilcoxon rank-sum test
Abundance in Group 1: increased abundance in Female Patients with PTC (G2)
| NCBI | Quality Control | Links |
|---|---|---|
| Rhodococcus | ||
| Ralstonia | ||
| Chryseobacterium | ||
| Burkholderia | ||
| Caballeronia | ||
| Paraburkholderia |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hormone endocrine,hormones,Hormone,hormone
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not specified
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Thyroid-Stimulating Hormone (TSH)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Thyroid-Stimulating Hormone (TSH) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Signature 1
Source: Figure 3a
Description: Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.
Abundance in Group 1: decreased abundance in Thyroid-Stimulating Hormone (TSH)
| NCBI | Quality Control | Links |
|---|---|---|
| Carnobacterium | ||
| Prevotella | ||
| clostridia UCG-014clostridia UCG-014 |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Triiodothyronine (T3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Triiodothyronine (T3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.
Abundance in Group 1: decreased abundance in Triiodothyronine (T3)
| NCBI | Quality Control | Links |
|---|---|---|
| Granulicatella |
Revision editor(s): Aleru Divine
Experiment 11
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Thyroxine (T4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Thyroxine (T4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.
Abundance in Group 1: decreased abundance in Thyroxine (T4)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Klebsiella |
Revision editor(s): Aleru Divine
Experiment 12
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Free Triiodothyronine (FT3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Free Triiodothyronine (FT3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.
Abundance in Group 1: increased abundance in Free Triiodothyronine (FT3)
| NCBI | Quality Control | Links |
|---|---|---|
| Treponema |
Revision editor(s): Aleru Divine
Experiment 13
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Free Thyroxine (FT4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.
Abundance in Group 1: increased abundance in Free Thyroxine (FT4)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3a
Description: Heatmap of Spearman’s correlation analysis showing the relationship between the specific bacterial and thyroid-related hormones.
Abundance in Group 1: decreased abundance in Free Thyroxine (FT4)
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella |
Revision editor(s): Aleru Divine
Experiment 14
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antibody antibodies,Antibody,antibody
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Anti-thyroid-stimulating receptors (Anti-TSHR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Anti-thyroid-stimulating receptors (Anti-TSHR) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3b
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.
Abundance in Group 1: decreased abundance in Anti-thyroid-stimulating receptors (Anti-TSHR)
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella | ||
| Burkholderia | ||
| Caballeronia | ||
| Paraburkholderia |
Revision editor(s): Aleru Divine
Experiment 15
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Anti-thyroid peroxidase (Anti-TPO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Anti-thyroid peroxidase (Anti-TPO) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3b
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.
Abundance in Group 1: decreased abundance in Anti-thyroid peroxidase (Anti-TPO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Selenomonas | ||
| Prevotella | ||
| Streptococcus | ||
| Parvimonas | ||
| Akkermansia | ||
| Bacteroides | ||
| Haemophilus | ||
| UCG-002UCG-002 |
Revision editor(s): Aleru Divine
Experiment 16
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Anti-thyroglobulin (Anti-TG)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Anti-thyroglobulin (Anti-TG) and microbial abundance in Papillary Thyroid Cancer (PTC) patients.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3b
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.
Abundance in Group 1: increased abundance in Anti-thyroglobulin (Anti-TG)
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingomonas | ||
| Rhodococcus | ||
| Ralstonia | ||
| Brevundimonas |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3b
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies.
Abundance in Group 1: decreased abundance in Anti-thyroglobulin (Anti-TG)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus | ||
| Akkermansia |
Revision editor(s): Aleru Divine
Experiment 17
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hormone endocrine,hormones,Hormone,hormone
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Triiodothyronine (T3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Triiodothyronine (T3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S5c
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.
Abundance in Group 1: decreased abundance in Triiodothyronine (T3)
| NCBI | Quality Control | Links |
|---|---|---|
| Granulicatella |
Revision editor(s): Aleru Divine
Experiment 18
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Free Triiodothyronine (FT3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Free Triiodothyronine (FT3) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S5c
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.
Abundance in Group 1: decreased abundance in Free Triiodothyronine (FT3)
| NCBI | Quality Control | Links |
|---|---|---|
| Granulicatella |
Revision editor(s): Aleru Divine
Experiment 19
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Free Thyroxine (FT4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Free Thyroxine (FT4) and different microbial genera in Papillary Thyroid Cancer (PTC) patients in the validation set.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S5c
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid-related hormones in the validation set.
Abundance in Group 1: increased abundance in Free Thyroxine (FT4)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia UCG-014Clostridia UCG-014 |
Revision editor(s): Aleru Divine
Experiment 20
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antibody antibodies,Antibody,antibody
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Anti-thyroid-stimulating receptors (Anti-TSHR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Anti-thyroid-stimulating receptors (Anti-TSHR) and microbial abundance in Papillary Thyroid Cancer (PTC) patients in the validation set.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S5d
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies in the validation set.
Abundance in Group 1: increased abundance in Anti-thyroid-stimulating receptors (Anti-TSHR)
| NCBI | Quality Control | Links |
|---|---|---|
| Leptotrichia |
Revision editor(s): Aleru Divine
Experiment 21
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Anti-thyroid peroxidase (Anti-TPO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The association between Anti-thyroid peroxidase (Anti-TPO) and microbial abundance in Papillary Thyroid Cancer (PTC) patients in the validation set.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S5d
Description: Heatmap of Spearman’s correlation analysis between the specific bacterial and thyroid diseases (AITD)-related antibodies in the validation set.
Abundance in Group 1: increased abundance in Anti-thyroid peroxidase (Anti-TPO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Haemophilus |
Revision editor(s): Aleru Divine
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
