Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis/Experiment 3
From BugSigDB
Needs review
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
- Metastatic colorectal cancer Metastatic colorectal cancer,metastatic colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No liver metastasis (NLM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Liver metastasis (LM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal patients with liver metastasis (LM) in the validation cohort (cohort 3)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- 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)
- Within 3 months prior to specimen collection.
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Figure 4e, 4f and Figure 5e
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.
Abundance in Group 1: increased abundance in Liver metastasis (LM)
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 4e, 4f and Figure 5e
Description: Taxonomic tree, histogram and heatmap (fig 5) displaying differentially abundant taxa in the cladogram in cohort 3.
Abundance in Group 1: decreased abundance in Liver metastasis (LM)
Revision editor(s): Aleru Divine
