Toward defining the autoimmune microbiome for type 1 diabetes/Experiment 2
From BugSigDB
Needs review
Subjects
- Location of subjects
- Finland
- 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
- Autoimmune disease Autoimmune disease,autoimmune disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Case 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at 1 year after birth.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Chi-Square
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, Matched on: "HLA-DQ genotype" 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.HLA-DQ genotype
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: increased abundance in Case 2
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: decreased abundance in Case 2
Revision editor(s): Aleru Divine
