Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Empty strings are not accepted.
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
- Lung
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung carcinoma
- 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
- cancerous site
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- diagnosis of lung cancer established by histological confirmation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
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
- 3.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 3
Description: Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups
Abundance in Group 1: increased abundance in cancerous site
| NCBI | Quality Control | Links |
|---|---|---|
| Mycobacteriales | ||
| Streptococcaceae | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Figure 3
Description: Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups
Abundance in Group 1: decreased abundance in cancerous site
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxellaceae | ||
| Staphylococcaceae | ||
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Empty strings are not accepted.
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Claregrieve1, Folakunmi, Tosin
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- paired contralateral non-cancerous site in lung cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- paired contralateral non-cancerous site samples from patients with diagnosis of lung cancer established by histological confirmation
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
Signature 1
Source: Figure 3
Description: Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups
Abundance in Group 1: increased abundance in paired contralateral non-cancerous site in lung cancer patients
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Figure 3
Description: Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups
Abundance in Group 1: decreased abundance in paired contralateral non-cancerous site in lung cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Lachnospiraceae | ||
| Moraxellaceae | ||
| Pseudomonadales |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Claregrieve1, Folakunmi, Tosin
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paired contralateral non-cancerous site (TN)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous site (T)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with diagnosis of lung cancer established by histological confirmation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
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
Signature 1
Source: Figure 3
Description: Differentially abundant taxa between T (patients in cancerous site) and TN (contralateral non-cancerous site) groups
Abundance in Group 1: increased abundance in cancerous site (T)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Candidatus Saccharibacteria | ||
| Dialister |
Experiment 4
Empty strings are not accepted.
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control group with no antibiotics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous site with no antibiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients who have diagnosis of lung cancer established by histological confirmation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Supplemental Figure S1
Description: Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics)
Abundance in Group 1: increased abundance in cancerous site with no antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Supplemental Figure S1
Description: Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics)
Abundance in Group 1: decreased abundance in cancerous site with no antibiotics
Revision editor(s): Claregrieve1, WikiWorks
Experiment 5
Empty strings are not accepted.
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control group with no antibiotics (No)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- contralateral non-cancerous site with no antibiotics (TNo)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- contralateral non-cancerous site samples from lung cancer patients who received no antibiotics in the prior three months
Lab analysis
Statistical Analysis
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
- unchanged
Signature 1
Source: supplementary figure 1
Description: Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics)
Abundance in Group 1: increased abundance in contralateral non-cancerous site with no antibiotics (TNo)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Neisseria | ||
| Neisseriaceae | ||
| Neisseriales | ||
| Staphylococcaceae | ||
| Staphylococcus |
Signature 2
Source: supplementary figure 1
Description: Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics)
Abundance in Group 1: decreased abundance in contralateral non-cancerous site with no antibiotics (TNo)
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- contralateral non-cancerous site with no antibiotics (TNo)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cancerous site with no antibiotics (To)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cancerous site samples from lung cancer patients who received no antibiotics in the prior three months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: supplementary figure 1
Description: Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and To (cancerous site samples of lung cancer patients who received no antibiotics prior to 3 months)
Abundance in Group 1: increased abundance in Cancerous site with no antibiotics (To)
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacteriaceae | ||
| Acidaminococcaceae | ||
| Phascolarctobacterium |
