The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-4-8
Curated date: 2024/03/18
Curator: Muqtadirat
Revision editor(s): Muqtadirat, Scholastica, Peace Sandy
Subjects
- Location of subjects
- China
- 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
- Ovary Animal ovary,Female gonad,Female organism genitalia gonad,Female organism genitalia gonada,Female organism reproductive system gonad,Female organism reproductive system gonada,Female reproductive system gonad,Female reproductive system gonada,Genitalia of female organism gonad,Genitalia of female organism gonada,Gonad of female organism genitalia,Gonad of female organism reproductive system,Gonad of female reproductive system,Gonad of genitalia of female organism,Gonad of reproductive system of female organism,Gonada of female organism genitalia,Gonada of female organism reproductive system,Gonada of female reproductive system,Gonada of genitalia of female organism,Gonada of reproductive system of female organism,Ovaries,Ovarium,Ovum-producing ovary,Reproductive system of female organism gonad,Reproductive system of female organism gonada,Ovary,ovary
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Ovarian cancer cancer of ovary,cancer of the ovary,malignant neoplasm of ovary,malignant neoplasm of the ovary,malignant ovarian neoplasm,malignant ovarian tumor,malignant ovary neoplasm,malignant tumor of ovary,malignant tumor of the ovary,malignant tumour of ovary,ovarian cancer,ovarian cancer, epithelial,ovarian malignant tumor,ovarian neoplasm,ovary cancer,ovary neoplasm,primary ovarian cancer,tumor of the ovary,Ovarian cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Immune-enriched subtype (clust2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Immune-deficient subtype (clust1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with the ovarian cancer subtype which is characterized by the lack of immune infiltration and high tumor purity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 191
- Group 1 sample size Number of subjects in the case (exposed) group
- 182
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- PCR
- 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
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-4-8
Source: Fig. 3C
Description: Significant differentially abundant taxonomic biomarkers between immune-deficient subtype (clust1) and immune-enriched subtype (clust2) identified by LEfSe
Abundance in Group 1: increased abundance in Immune-deficient subtype (clust1)
Revision editor(s): Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-4-8
Source: Fig. 3C
Description: Significant differentially abundant taxonomic biomarkers between immune-deficient subtype (clust1) and immune-enriched subtype (clust2) identified by LEfSe
Abundance in Group 1: decreased abundance in Immune-deficient subtype (clust1)
Revision editor(s): Scholastica