Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients/Experiment 3

From BugSigDB


Reviewed Marked as Reviewed by Folakunmi on 2024-2-21

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256, Folakunmi

Subjects

Location of subjects
United States of America
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
Colorectal mucosa Colorectal mucosa,colorectal mucosa
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Normal samples free from Colorectal Cancer
Group 1 name Corresponds to the case (exposed) group for case-control studies
European American Samples with Colorectal Cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
European American Patients with colorectal cancer
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
19

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
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

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-20

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256

Source: Figure 2C

Description: Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.

Abundance in Group 1: increased abundance in European American Samples with Colorectal Cancer

NCBI Quality ControlLinks
Massilia

Revision editor(s): Chloe 256

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-20

Curated date: 2023/10/13

Curator: Chloe 256

Revision editor(s): Chloe 256, Iram jamshed

Source: Figure 2C

Description: Figure 2C shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in European Americans.

Abundance in Group 1: decreased abundance in European American Samples with Colorectal Cancer

NCBI Quality ControlLinks
Gemmiger formicilis
Geobacter
Segatella copri
Mediterraneibacter gnavus

Revision editor(s): Chloe 256, Iram jamshed