Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Folakunmi on 2024-2-4

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

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 Pulmo,Lung,lung
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
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
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
none

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Mycobacteriales
Streptococcaceae
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Moraxellaceae
Staphylococcaceae
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks