Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites/Experiment 1
Curated date: 2024/03/21
Curator: Omojokunoluwatomisin
Revision editor(s): WikiWorks, Scholastica, Omojokunoluwatomisin
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung cancer alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Benign pulmonary diseases (N group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lung cancer (L group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lung cancer patients graded according to the American Thoracic Society/ European Respiratory Society (ATS/ERS) five level classification method for pulmonary ventilation impairment and divided into 3 groups, including 20 patients with normal lung ventilation, 23 patients with mild pulmonary ventilation dysfunction and 12 patients with moderate or above pulmonary ventilation dysfunction.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 55
- 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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Curated date: 2024/03/21
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Scholastica, WikiWorks
Source: figure 2b
Description: Differential taxa at the genus level analyzed by linear discriminant analysis (LDA) scores in lung cancer patients (C) versus benign diseases patients(N)
Abundance in Group 1: increased abundance in Lung cancer (L group)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Oscillospiraceae |
Revision editor(s): Omojokunoluwatomisin, Scholastica, WikiWorks
Signature 2
Curated date: 2024/03/21
Curator: Omojokunoluwatomisin
Revision editor(s): WikiWorks, Scholastica, Omojokunoluwatomisin, Tosin
Source: figure 2b
Description: Differential taxa at the genus level analyzed by linear discriminant analysis (LDA) scores in lung cancer patients (C) versus benign diseases patients(N)
Abundance in Group 1: decreased abundance in Lung cancer (L group)
Revision editor(s): WikiWorks, Scholastica, Omojokunoluwatomisin, Tosin
