-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Israel
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- pancreatic carcinoma cancer of pancreas,cancer of the pancreas,carcinoma of exocrine pancreas,carcinoma of pancreas,carcinoma of the pancreas,exocrine cancer,exocrine pancreas carcinoma,exocrine pancreatic carcinoma,pancreas cancer,pancreas carcinoma,pancreatic cancer,pancreatic cancer (not islets),pancreatic carcinoma,pancreatic carcinoma, familial
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pancreatic cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 8 weeks
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 2a
Description: Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.
Abundance in Group 1: increased abundance in Pancreatic cancer patients
NCBI | Quality Control | Links |
---|---|---|
Akkermansia | ||
Bacteroidales | ||
Megasphaera | ||
Odoribacter | ||
Veillonellaceae | ||
Lachnospiraceae bacterium |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Signature 2
Source: Figure 2a
Description: Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.
Abundance in Group 1: decreased abundance in Pancreatic cancer patients
NCBI | Quality Control | Links |
---|---|---|
Anaerostipes | ||
Eubacteriales | ||
Faecalibacterium | ||
Oscillospiraceae | ||
Subdoligranulum | ||
Clostridium sp. | ||
Oscillospiraceae bacterium | ||
uncultured bacterium |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Experiment 3
Curated date: 2021/02/04
Curator: Yu Wang
Revision editor(s): Fatima, Yu Wang, Claregrieve1, WikiWorks
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NBO PC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BO PC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bile duct-obstructed pancreatic cancer patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 2
Source: Figure 3b
Description: Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.
Abundance in Group 1: increased abundance in BO PC
NCBI | Quality Control | Links |
---|---|---|
Selenomonadales | ||
Veillonellaceae | ||
Prevotella |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Experiment 4
Subjects
- Host species Species from which microbiome was sampled (if applicable)
- Not specified
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NBO PC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Non-Bile duct-obstructed pancreatic cancer patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3c
Description: Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.
Abundance in Group 1: decreased abundance in NBO PC
NCBI | Quality Control | Links |
---|---|---|
Faecalibacterium | ||
Oscillospiraceae | ||
Clostridium sp. 001 | ||
Mollicutes |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Signature 2
Source: Figure 3c
Description: Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.
Abundance in Group 1: increased abundance in NBO PC
NCBI | Quality Control | Links |
---|---|---|
Akkermansia | ||
Bacteroidales |
Revision editor(s): Fatima, Yu Wang, Claregrieve1