Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients
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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
- Egypt
- 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
- 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
- Normal samples free from Colorectal Cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Egyptian Samples with Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Egyptian Patients with colocrectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-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
Curated date: 2023/10/12
Curator: Chloe 256
Revision editor(s): WikiWorks, Peace Sandy, Folakunmi, Chloe 256
Source: Figure 2A
Description: Fig.2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in Egyptians.
Abundance in Group 1: increased abundance in Egyptian Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Abyssicoccus albus | ||
| Bifidobacterium pseudolongum | ||
| Corynebacterium kroppenstedtii | ||
| Cutibacterium acnes | ||
| Eubacteriales | ||
| Kocuria | ||
| Lactobacillus helveticus | ||
| Tissierella creatinophila |
Revision editor(s): WikiWorks, Peace Sandy, Folakunmi, Chloe 256
Signature 2
Source: Figure 2A
Description: Figure 2A shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in egyptians.
Abundance in Group 1: decreased abundance in Egyptian Samples with Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Exiguobacterium | ||
| Kocuria palustris | ||
| Micrococcus | ||
| Neisseria | ||
| Pseudomonas viridiflava | ||
| Rothia aeria |
Revision editor(s): Chloe 256, Peace Sandy, WikiWorks
Experiment 2
Empty strings are not accepted.
Curated date: 2023/10/13
Curator:
Revision editor(s):
Subjects
- Location of subjects
- United States of America
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- African American Samples with Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- African American Patients with Colorectal cancer.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
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
Source: Figure 2B
Description: Figure 2B shows histogram of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African Americans.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium perfringens | ||
| Gardnerella | ||
| Granulicatella | ||
| Rhodobacter |
Signature 2
Source: Figure 2B
Description: Figure 2B shows histograms of differential microbial taxa, at the species level, between tumor (CRC) and normal samples in African American
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Bradyrhizobium |
Experiment 3
Empty strings are not accepted.
Curated date: 2023/10/13
Curator:
Revision editor(s):
Subjects
- 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
Statistical Analysis
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
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
| NCBI | Quality Control | Links |
|---|---|---|
| Massilia |
Signature 2
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
| NCBI | Quality Control | Links |
|---|---|---|
| Gemmiger formicilis | ||
| Geobacter | ||
| Segatella copri | ||
| Mediterraneibacter gnavus |
Revision editor(s): Chloe 256, Iram jamshed, WikiWorks
Experiment 4
Curated date: 2023/11/06
Curator:
Revision editor(s):
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Population Population,population
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- KeNyaN, African American and Egyptians patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of European American
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- sample of European Americans patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 53
Lab analysis
Statistical Analysis
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
Source: Figure 3
Description: Differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroplasma | ||
| Bacteroides ovatus | ||
| Clostridium perfringens | ||
| Comamonadaceae | ||
| Eggerthella lenta | ||
| Flexispira | ||
| Mycoplasma | ||
| Streptococcus | ||
| f_S24_7_9_s_f_S24_7_9_s_ | ||
| Lactobacillus iners |
Revision editor(s): WikiWorks, Folakunmi, Chloe 256, MyleeeA
Experiment 5
Curated date: 2023/11/14
Curator:
Revision editor(s):
Subjects
- Location of subjects
- Kenya
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Egyptian, African American and European American Patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of kenyans
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor samples of kenyan patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 54
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
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
Source: Figure 3
Description: differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in
Revision editor(s): WikiWorks, Folakunmi, Joan Chuks, Chloe 256, MyleeeA
Experiment 6
Curated date: 2023/11/14
Curator:
Revision editor(s):
Subjects
- Location of subjects
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Egyptian, Kenyan and European American patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of African Americans
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sample of African American patients
Lab analysis
Statistical Analysis
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
Source: Figure 3
Description: differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in
Revision editor(s): WikiWorks, Folakunmi, Chloe 256, MyleeeA
Experiment 7
Curated date: 2023/11/15
Curator:
Revision editor(s):
Subjects
- Location of subjects
- Egypt
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- African American, Kenya and European American patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor samples of Egyptians
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- sample of Egyptian patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 55
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
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
Source: Figure 3
Description: differential microbial taxa between tumor (CRC) samples of different races at the species level
Abundance in Group 1: increased abundance in
Revision editor(s): WikiWorks, Folakunmi, Chloe 256, MyleeeA
