Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in 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.
Curated date: 2022/06/12
Curator: Jeshudy
Revision editor(s): WikiWorks, Jeshudy, Atrayees, Ifeanyisam
Subjects
- Location of subjects
- Japan
- 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 carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control (normal and a few polyps)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- stage I/II (SI/II)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- stage I and II CRCs
- Group 0 sample size Number of subjects in the control (unexposed) group
- 251
- Group 1 sample size Number of subjects in the case (exposed) group
- 111
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.005
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: increased abundance in stage I/II (SI/II)
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in stage I/II (SI/II)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum subsp. longum | ||
| Lachnospira eligens | ||
| Lachnospira multipara |
Experiment 2
Empty strings are not accepted.
Curated date: 2022/06/12
Curator: Jeshudy
Revision editor(s): WikiWorks, Jeshudy, Atrayees, Ifeanyisam
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- stage III/IV (SIII/IV)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- stage III and IV CRCs
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Phylum distribution of the number of species that are either elevated or depleted in each of the four stages compared to the healthy controls.
Abundance in Group 1: increased abundance in stage III/IV (SIII/IV)
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in stage III/IV (SIII/IV)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira eligens | ||
| Lachnospira multipara |
Experiment 3
Empty strings are not accepted.
Curated date: 2022/06/12
Curator: Jeshudy
Revision editor(s): WikiWorks, Jeshudy, Atrayees, Ifeanyisam
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- S0
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- stage 0/pTis CRC (S0)
- Group 1 sample size Number of subjects in the case (exposed) group
- 73
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: increased abundance in S0
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in S0
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum subsp. longum | ||
| Lachnospira multipara | ||
| Lachnospira eligens |
Experiment 4
Empty strings are not accepted.
Curated date: 2022/06/12
Curator: Jeshudy
Revision editor(s): WikiWorks, Jeshudy, Atrayees, Ifeanyisam
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- multiple polypoid adenomas with low- grade dysplasia (MP, more than three adenomas, mostly more than five adenomas)
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: increased abundance in MP
| NCBI | Quality Control | Links |
|---|---|---|
| Lancefieldella parvula | ||
| Fusobacterium nucleatum | ||
| Schaalia odontolytica | ||
| Phascolarctobacterium succinatutens | ||
| Selenomonas sputigena | ||
| Oleidesulfovibrio vietnamensis |
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in MP
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum subsp. longum | ||
| Lachnospira multipara | ||
| Lachnospira eligens |
