Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-3-26
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
- Mucosa Mucosa of organ,Mucosa of organ part,Mucosal region,Mucous membrane,Organ mucosa,Region of mucosa,Tunica mucosa,Mucosa,mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colon carcinoma carcinoma of colon,carcinoma of the colon,colon cancer,colon carcinoma,colonic carcinoma,Colon carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in this group had radical resection of colon cancer tumors and were diagnosed with colon cancer for the first time, confirmed by colonoscopy pathology.
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-26
Source: Figure 2f
Description: Distribution histogram of LDA values of different species (LDA > 3).
Abundance in Group 1: increased abundance in Tumor group
Revision editor(s): Victoria
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-26
Source: Figure 2f
Description: Distribution histogram of LDA values of different species (LDA > 3).
Abundance in Group 1: decreased abundance in Tumor group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides uniformis | ||
| Bifidobacterium breve | ||
| Bifidobacterium pseudocatenulatum | ||
| Phocaeicola dorei | ||
| Phocaeicola vulgatus |
Revision editor(s): Victoria
