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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
Subjects
- Location of subjects
- Finland
- Germany
- United Kingdom
- 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
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic eczema allergic,allergic dermatitis,allergic form of dermatitis,Atopic Dermatitides,Atopic Dermatitis,Atopic dermatitis,atopic dermatitis and related conditions,Atopic dermatitis and related conditions (disorder),atopic eczema,Atopic Neurodermatitides,Atopic Neurodermatitis,Atopic neurodermatitis,Besnier's prurigo,Dermatitides, Atopic,Dermatitis, Atopic,Disseminated Neurodermatitides,Disseminated Neurodermatitis,eczema,Eczema, Atopic,Eczema, Infantile,eczematous dermatitis,Infantile Eczema,Neurodermatitides, Atopic,Neurodermatitides, Disseminated,Neurodermatitis, Atopic,Neurodermatitis, Disseminated,OTHER ATOPIC DERMATITIS,Other atopic dermatitis and related conditions
- 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
- adult with atopic dermatitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- adult with atopic dermatitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 115
- Group 1 sample size Number of subjects in the case (exposed) group
- 82
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 1c, Supplemental Figure 3b
Description: Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls
Abundance in Group 1: increased abundance in adult with atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Staphylococcus aureus |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 1c, Supplemental Figure 3b
Description: Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls
Abundance in Group 1: decreased abundance in adult with atopic dermatitis
NCBI | Quality Control | Links |
---|---|---|
Burkholderia sp. | ||
Finegoldia sp. | ||
Staphylococcus sp. | ||
Lactobacillus sp. | ||
Pelomonas sp. | ||
Cutibacterium acnes |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- psoriasis Other and unspecified pityriasis,OTHER PSORIASIS,Other psoriasis and similar disorders,Other psoriasis and similar disorders (disorder),Other psoriasis and similar disorders excluding psoriatic arthropathy,Palmoplantaris Pustulosis,PITYRIASIS NEC & NOS,PSORIAS RELATED DIS NEC,Psoriases,psoriasis,Psoriasis and similar disorders,Psoriasis and similar disorders (disorder),Psoriasis and similar disorders (navigational concept),Psoriasis and similar disorders NOS,Psoriasis and similar disorders NOS (disorder),Pustular Psoriasis of Palms and Soles,PUSTULAR PSORIASIS OF PALMS SOLES,Pustulosis of Palms and Soles,PUSTULOSIS OF PALMS SOLES,Pustulosis Palmaris et Plantaris
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adult with psoriasis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- adult with psoriasis
- Group 1 sample size Number of subjects in the case (exposed) group
- 119
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 1c, Supplemental Figure 3b
Description: Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls
Abundance in Group 1: increased abundance in adult with psoriasis
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium simulans | ||
Finegoldia sp. | ||
Neisseriaceae | ||
Corynebacterium kroppenstedtii | ||
Anaerococcus sp. |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 1c, Supplemental Figure 3b
Description: Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls
Abundance in Group 1: decreased abundance in adult with psoriasis
NCBI | Quality Control | Links |
---|---|---|
Burkholderia sp. | ||
Lactobacillus sp. | ||
Pelomonas sp. |
Revision editor(s): WikiWorks