The human gut microbiome as a screening tool for colorectal cancer/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-19

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Peace Sandy

Subjects

Location of subjects
Canada
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
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
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
Healthy Controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
carcinoma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with colonic adenocarcinoma
Group 0 sample size Number of subjects in the control (unexposed) group
30
Group 1 sample size Number of subjects in the case (exposed) group
30

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
2.5


Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-19

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks, Peace Sandy

Source: Supplemental Figure 2 and text

Description: LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.

Abundance in Group 1: increased abundance in carcinoma

NCBI Quality ControlLinks
Enterobacteriaceae
Fusobacterium
Lachnospiraceae
Porphyromonas
Clostridium
Porphyromonadaceae

Revision editor(s): WikiWorks, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-19

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks, Peace Sandy

Source: Supplemental Figure 2 and text

Description: LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.

Abundance in Group 1: decreased abundance in carcinoma

NCBI Quality ControlLinks
Bacteroides
Eubacteriales
Lachnospiraceae
Staphylococcus
Clostridium

Revision editor(s): WikiWorks, Peace Sandy