Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Empty strings are not accepted.
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
- Intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy volunteers (swc)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients (swp)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, diagnosed with colorectal cancer (swp = gut swab)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- 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
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Sanger
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
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
Signature 1
Source: Figure 4A
Description: Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.
Abundance in Group 1: decreased abundance in CRC patients (swp)
NCBI | Quality Control | Links |
---|---|---|
Anaerostipes | ||
Catenibacterium | ||
Faecalibacterium | ||
Blautia | ||
Gardnerella | ||
Bifidobacterium | ||
Lachnospira |
Signature 2
Source: Figure 4A
Description: Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.
Abundance in Group 1: increased abundance in CRC patients (swp)
NCBI | Quality Control | Links |
---|---|---|
Catonella | ||
Fusobacterium | ||
Gemella | ||
Klebsiella | ||
Mogibacterium | ||
Peptostreptococcus | ||
Porphyromonas | ||
Selenomonas | ||
Filifactor |
Experiment 2
Empty strings are not accepted.
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paracancerous tissue (pa10t)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous tissue (cat)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, colorectal cancer tissue Note: group 0 = paracancerous tissue 10-20 cm from cancerous tissue
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "patient" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.patient
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 3
Description: Phylotypes significantly different between cat and pa10t.
Abundance in Group 1: decreased abundance in cancerous tissue (cat)
NCBI | Quality Control | Links |
---|---|---|
Bacillus | ||
Paraprevotella | ||
Phascolarctobacterium | ||
Parabacteroides | ||
Faecalibacterium | ||
Alphaproteobacteria | ||
Methylobacterium | ||
Acidocella |
Experiment 3
Empty strings are not accepted.
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paracancerous tissue (pa2t)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, cancerous tissue. Note: Group 0 = paracancerous tissue 2-5 cm from cancerous tissue
Lab analysis
Statistical Analysis
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
Experiment 4
Empty strings are not accepted.
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy volunteers (stc)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients (stp)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, diagnosed with colorectal cancer (stp = stool sample)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
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
Signature 1
Source: Figure 4B
Description: Figure 4. Relative abundance of significantly different genera between CRC patients and healthy controls. Genera differing between stp and stc.
Abundance in Group 1: increased abundance in CRC patients (stp)
NCBI | Quality Control | Links |
---|---|---|
Anaerococcus | ||
Anaerotruncus | ||
Collinsella | ||
Eubacterium | ||
Mogibacterium | ||
Slackia | ||
Paraprevotella | ||
Desulfovibrio | ||
Porphyromonas | ||
Peptostreptococcus |