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Google Keyword Rankings for : enrichment p value
1
Statistics for Enrichment Analysis | Metascape Blog
https://metascape.org/blog/?p=122
p-values are often provided in logarithmic based ten (“LogP” in Metascape). Therefore, a more negative p-value indicates the less chance the ...
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https://metascape.org/blog/?p=122
p-values are often provided in logarithmic based ten (“LogP” in Metascape). Therefore, a more negative p-value indicates the less chance the ...
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2
Why do I need to correct my p-values? - Advaita Bioinformatics
https://advaitabio.com/ivariantguide/p-value/
For example, if there are 5 differentially expressed (DE) genes on pathway X out of 100 DE genes in the dataset, the over-enrichment p-value for pathway X ...
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https://advaitabio.com/ivariantguide/p-value/
For example, if there are 5 differentially expressed (DE) genes on pathway X out of 100 DE genes in the dataset, the over-enrichment p-value for pathway X ...
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3
Methods for Determining the Statistical Significance of ... - NCBI
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284693/
Usually, the significance of enrichment or depletion scores is based on simple statistical models and on the membership of genes in different classifications.
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284693/
Usually, the significance of enrichment or depletion scores is based on simple statistical models and on the membership of genes in different classifications.
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4
gsEasy
https://cran.r-project.org/web/packages/gsEasy/vignettes/gsEasy-guide.html
p : a numeric value used to exponentiate the enrichment scores given by r , with higher values having the effect of increasing the weight on the ...
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https://cran.r-project.org/web/packages/gsEasy/vignettes/gsEasy-guide.html
p : a numeric value used to exponentiate the enrichment scores given by r , with higher values having the effect of increasing the weight on the ...
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5
GO enrichment analysis - Gene Ontology
http://geneontology.org/docs/go-enrichment-analysis/
P-value is the probability or chance of seeing at least x number of genes out of the total n genes in the list annotated to a particular GO term, ...
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http://geneontology.org/docs/go-enrichment-analysis/
P-value is the probability or chance of seeing at least x number of genes out of the total n genes in the list annotated to a particular GO term, ...
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6
While doing GO enrichment analysis, what to choose : p value ...
https://www.researchgate.net/post/While_doing_GO_enrichment_analysis_what_to_choose_p_value_or_adjusted_p_value_and_why
(ii) you should not test hypotheses, because the enrichment analysis is an exploratory method. The p-value (adjusted or unadjuted) can be used to rank the ...
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https://www.researchgate.net/post/While_doing_GO_enrichment_analysis_what_to_choose_p_value_or_adjusted_p_value_and_why
(ii) you should not test hypotheses, because the enrichment analysis is an exploratory method. The p-value (adjusted or unadjuted) can be used to rank the ...
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7
Pathway Enrichment Analysis (PEA) - Read the Docs
https://paintomics.readthedocs.io/en/latest/4_1_pathway_enrichment/
As a general rule, a p-value of 0.05 is accepted as the threshold indicating a statistically significant association. From this analysis the application ranks ...
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https://paintomics.readthedocs.io/en/latest/4_1_pathway_enrichment/
As a general rule, a p-value of 0.05 is accepted as the threshold indicating a statistically significant association. From this analysis the application ranks ...
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8
Pathway Analysis: ANOVA vs. Enrichment Analysis – Partek Inc
https://www.partek.com/pathway-analysis-anova-vs-enrichment-analysis/
Most researchers transform the p-value into an enrichment score (enrichment score = -ln(p-value)) to make it easier to read (e.g., 6.9, ...
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https://www.partek.com/pathway-analysis-anova-vs-enrichment-analysis/
Most researchers transform the p-value into an enrichment score (enrichment score = -ln(p-value)) to make it easier to read (e.g., 6.9, ...
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9
Gene Set Enrichment Analysis - Pathway Commons
https://www.pathwaycommons.org/guide/primers/data_analysis/gsea/
In this context, a p-value assigned to a gene can be interpreted as the probability of a difference in gene expression between groups at least as extreme as ...
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https://www.pathwaycommons.org/guide/primers/data_analysis/gsea/
In this context, a p-value assigned to a gene can be interpreted as the probability of a difference in gene expression between groups at least as extreme as ...
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10
Robust and accurate data enrichment statistics via distribution ...
https://academic.oup.com/bioinformatics/article/26/21/2752/213760
By definition, a P-value associated with a score is the probability of that score or better arising purely by chance. We tested the accuracy of reported P- ...
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https://academic.oup.com/bioinformatics/article/26/21/2752/213760
By definition, a P-value associated with a score is the probability of that score or better arising purely by chance. We tested the accuracy of reported P- ...
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11
Gene set enrichment analysis: A knowledge-based ... - PNAS
https://www.pnas.org/doi/10.1073/pnas.0506580102
In these cases, a P value can be estimated by permuting the genes, with the result that genes are randomly assigned to the sets while maintaining their size.
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https://www.pnas.org/doi/10.1073/pnas.0506580102
In these cases, a P value can be estimated by permuting the genes, with the result that genes are randomly assigned to the sets while maintaining their size.
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12
Table of Contents - GSEA
https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm
The nominal p value estimates the statistical significance of the enrichment score for a single gene set. However, when you are evaluating multiple gene ...
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https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm
The nominal p value estimates the statistical significance of the enrichment score for a single gene set. However, when you are evaluating multiple gene ...
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13
Chapter 5 Overview of enrichment analysis - YuLab@SMU
https://yulab-smu.top/biomedical-knowledge-mining-book/enrichment-overview.html
The p-value of the ES is calculated using a permutation test. Specifically, we permute the gene labels of the gene list L and recompute the ES of the gene set ...
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https://yulab-smu.top/biomedical-knowledge-mining-book/enrichment-overview.html
The p-value of the ES is calculated using a permutation test. Specifically, we permute the gene labels of the gene list L and recompute the ES of the gene set ...
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14
Gene set enrichment analysis with topGO - Bioconductor
https://bioconductor.org/packages/devel/bioc/vignettes/topGO/inst/doc/topGO.pdf
The function assumes that the provided argument is a named vector of p-values. With the help of this function we can see that there are 50 genes.
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https://bioconductor.org/packages/devel/bioc/vignettes/topGO/inst/doc/topGO.pdf
The function assumes that the provided argument is a named vector of p-values. With the help of this function we can see that there are 50 genes.
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15
Nine quick tips for pathway enrichment analysis - PLOS
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010348
To alleviate this issue, we recommend using the adjusted p-value for multiple testing, sometimes also called corrected p-value and indicated as ...
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https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010348
To alleviate this issue, we recommend using the adjusted p-value for multiple testing, sometimes also called corrected p-value and indicated as ...
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16
Gene Set Analysis: Challenges, Opportunities, and Future ...
https://www.frontiersin.org/articles/10.3389/fgene.2020.00654/full
Next, genes with a adjusted p-value smaller than a given threshold are predicted ... Gene set analysis, also know as enrichment analysis, is an attempt to ...
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https://www.frontiersin.org/articles/10.3389/fgene.2020.00654/full
Next, genes with a adjusted p-value smaller than a given threshold are predicted ... Gene set analysis, also know as enrichment analysis, is an attempt to ...
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17
The Limitations of Simple Gene Set Enrichment Analysis ...
https://arxiv.org/pdf/1110.4128
enrichment scores, p- and q-values for each gene set. In order to make a fair comparison of both methods we computed the GSEA q-values using exactly the ...
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https://arxiv.org/pdf/1110.4128
enrichment scores, p- and q-values for each gene set. In order to make a fair comparison of both methods we computed the GSEA q-values using exactly the ...
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18
Determining enrichment of p-values - Cross Validated
https://stats.stackexchange.com/questions/172574/determining-enrichment-of-p-values
› questions › determinin...
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https://stats.stackexchange.com/questions/172574/determining-enrichment-of-p-values
› questions › determinin...
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19
Fast gene set enrichment analysis | bioRxiv
https://www.biorxiv.org/content/10.1101/060012v2.full
Here we present FGSEA method that is able to estimate arbitrarily low GSEA P-values with a higher accuracy and much faster compared to other ...
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https://www.biorxiv.org/content/10.1101/060012v2.full
Here we present FGSEA method that is able to estimate arbitrarily low GSEA P-values with a higher accuracy and much faster compared to other ...
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20
Gene Ontology (GO) Enrichment - VEuPathDB Workshop
https://workshop.veupathdb.org/current/exercises/Day1/GO-Enrichment.pdf
Benjamini-Hochberg false discovery rate (FDR) or Bonferroni adjusted p-value. 1. In order to run a GO enrichment analysis, you need a list of genes to test.
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https://workshop.veupathdb.org/current/exercises/Day1/GO-Enrichment.pdf
Benjamini-Hochberg false discovery rate (FDR) or Bonferroni adjusted p-value. 1. In order to run a GO enrichment analysis, you need a list of genes to test.
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21
Gene Ontology and KEGG Enrichment Analysis - GitHub Pages
https://ucdavis-bioinformatics-training.github.io/2019_March_UCSF_mRNAseq_Workshop/differential_expression/enrichment.html
This contains the genes, the score for each gene (here we use the p-value from the DE test), the GO terms associated with each gene, and the ontology to be ...
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https://ucdavis-bioinformatics-training.github.io/2019_March_UCSF_mRNAseq_Workshop/differential_expression/enrichment.html
This contains the genes, the score for each gene (here we use the p-value from the DE test), the GO terms associated with each gene, and the ontology to be ...
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22
Gene Ontology Enrichment Analysis (GOEAST) - Omics Lab
http://omicslab.genetics.ac.cn/GOEAST/faq.php
. The smaller the p-value is, the more significant the GO term is enriched in your dataset. Other statistical test is also supported to calculate p- ...
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http://omicslab.genetics.ac.cn/GOEAST/faq.php
. The smaller the p-value is, the more significant the GO term is enriched in your dataset. Other statistical test is also supported to calculate p- ...
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23
PSEA-Quant: A Protein Set Enrichment Analysis on Label ...
https://pubs.acs.org/doi/10.1021/pr500473n
PSEA-Quant uses a variety of approaches to estimate the statistical significance of protein sets in a given data set and assigns them p-values.
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https://pubs.acs.org/doi/10.1021/pr500473n
PSEA-Quant uses a variety of approaches to estimate the statistical significance of protein sets in a given data set and assigns them p-values.
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24
How to calculate enrichment P-value? - Biostars
https://www.biostars.org/p/176563/
Feb 11, 2016
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https://www.biostars.org/p/176563/
Feb 11, 2016
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25
2. Gene-enrichment and Functional Annotation Analysis - DAVID
https://david.ncifcrf.gov/helps/functional_annotation.html
It ranges from 0 to 1. Fisher Exact p-value = 0 represents perfect enrichment. Usually p-value is equal or smaller than 0.05 to be considered ...
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https://david.ncifcrf.gov/helps/functional_annotation.html
It ranges from 0 to 1. Fisher Exact p-value = 0 represents perfect enrichment. Usually p-value is equal or smaller than 0.05 to be considered ...
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26
ShinyGO 0.76.3
http://bioinformatics.sdstate.edu/go/
When users select "Sort by Fold Enrichment", the minimum pathway size is raised ... Otherwise this gene is ignored in the calculation of P values based on ...
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http://bioinformatics.sdstate.edu/go/
When users select "Sort by Fold Enrichment", the minimum pathway size is raised ... Otherwise this gene is ignored in the calculation of P values based on ...
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27
Data Correlation Details: Enrichment Analysis - Illumina
https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote-data-correlation-enrichment.pdf
An SNV bioset from a genome-wide association study (GWAS) will contain ranked SNVs with associated p-values. In summary (Figure 1), biosets may contain one of ...
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https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote-data-correlation-enrichment.pdf
An SNV bioset from a genome-wide association study (GWAS) will contain ranked SNVs with associated p-values. In summary (Figure 1), biosets may contain one of ...
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28
Gene set enrichment analysis - Wikipedia
https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis
Gene set enrichment analysis (GSEA) is a method to identify classes of genes or proteins that ... The P value is determined by comparison to the null distribution.
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https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis
Gene set enrichment analysis (GSEA) is a method to identify classes of genes or proteins that ... The P value is determined by comparison to the null distribution.
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29
Gene List Analysis Page Help - PantherDB.org
http://www.pantherdb.org/tips/tips_geneListAnalysis.jsp
Upload a list of genes/proteins, together with values (gene expression, protein expression, etc.), and run the enrichment test to evaluate likelihood of the ...
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http://www.pantherdb.org/tips/tips_geneListAnalysis.jsp
Upload a list of genes/proteins, together with values (gene expression, protein expression, etc.), and run the enrichment test to evaluate likelihood of the ...
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30
Gene Set Enrichment Analysis (GSEA) - OmicsBox User Manual
https://manual.omicsbox.biobam.com/user-manual/omicsbox-modules/module-functional-analysis/functional-analysis-(side-panel)/enrichment-analysis/gene-set-enrichment-analysis-(gsea)
Filtering. Only IDs with a higher p-value or FDR than the filter value will be shown. Note that FDR is the corrected p-value for multiple testing ...
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https://manual.omicsbox.biobam.com/user-manual/omicsbox-modules/module-functional-analysis/functional-analysis-(side-panel)/enrichment-analysis/gene-set-enrichment-analysis-(gsea)
Filtering. Only IDs with a higher p-value or FDR than the filter value will be shown. Note that FDR is the corrected p-value for multiple testing ...
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31
Practicals - Gene enrichment statistics - pedagogix
http://pedagogix-tagc.univ-mrs.fr/courses/ASG1/practicals/go_statistics_td/go_statistics_td_2015.html
Computing the hypergeometric P-value. The P-value is the probability to observe at least “x” marked balls in the selection. Compute the P-value ...
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http://pedagogix-tagc.univ-mrs.fr/courses/ASG1/practicals/go_statistics_td/go_statistics_td_2015.html
Computing the hypergeometric P-value. The P-value is the probability to observe at least “x” marked balls in the selection. Compute the P-value ...
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32
Gene Set Enrichment - an overview | ScienceDirect Topics
https://www.sciencedirect.com/topics/medicine-and-dentistry/gene-set-enrichment
GSEA approach is similar to SEA, i.e., the analysis of each annotation term separately, and uses a distinct algorithm to calculate enrichment P-values.
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https://www.sciencedirect.com/topics/medicine-and-dentistry/gene-set-enrichment
GSEA approach is similar to SEA, i.e., the analysis of each annotation term separately, and uses a distinct algorithm to calculate enrichment P-values.
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33
Pathway enrichment algorithms - ipavs tutorials - Google Sites
https://sites.google.com/a/cidms.org/ipavs_tutorials/pathway-analysis-visualization-and-data-manipulation-tools/pathway-enrichment-algorithms
The p-value associated with a pathway in enrichment analysis is a measure that tell that association between a selected genes from the experimental list and ...
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https://sites.google.com/a/cidms.org/ipavs_tutorials/pathway-analysis-visualization-and-data-manipulation-tools/pathway-enrichment-algorithms
The p-value associated with a pathway in enrichment analysis is a measure that tell that association between a selected genes from the experimental list and ...
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34
Tutorial: enrichment analysis - RPubs
https://rpubs.com/jrgonzalezISGlobal/enrichment
Overview of existing methods for enrichment analysis of gene expression data ... Fisher's Exact Test for Count Data data: deTable p-value ...
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https://rpubs.com/jrgonzalezISGlobal/enrichment
Overview of existing methods for enrichment analysis of gene expression data ... Fisher's Exact Test for Count Data data: deTable p-value ...
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35
g:Profiler – a web server for functional enrichment analysis ...
https://biit.cs.ut.ee/gprofiler/page/docs
The y-axis shows the adjusted enrichment p-values in negative log10 scale. The light circles represent insignificant terms (if available).
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https://biit.cs.ut.ee/gprofiler/page/docs
The y-axis shows the adjusted enrichment p-values in negative log10 scale. The light circles represent insignificant terms (if available).
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36
Gene Set Enrichment Analysis (GSEA) - PRO Feature
http://docs.blast2go.com/user-manual/analysis-menu/gene-set-enrichment-analysis-(gsea)-pro-feature
Results. Once completed the results table will be shown in a new tab (see image below), where the adjusted p-values of each annotation above ...
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http://docs.blast2go.com/user-manual/analysis-menu/gene-set-enrichment-analysis-(gsea)-pro-feature
Results. Once completed the results table will be shown in a new tab (see image below), where the adjusted p-values of each annotation above ...
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37
Bayesian functional enrichment analysis for the Reactome ...
https://www.tandfonline.com/doi/full/10.1080/24754269.2017.1387444
The hypergeometric P value has been widely used to investigate whether genes from predefined functional terms, e.g., Reactome, are enriched in the DE genes.
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https://www.tandfonline.com/doi/full/10.1080/24754269.2017.1387444
The hypergeometric P value has been widely used to investigate whether genes from predefined functional terms, e.g., Reactome, are enriched in the DE genes.
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38
Introduction to Statistical Methods for Analyzing Large Data Sets
https://www.science.org/doi/10.1126/scisignal.2001966
GSEA is a statistical functional enrichment analysis commonly applied to ... the probability (P value) of observing measurements in that range (Slide 6).
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https://www.science.org/doi/10.1126/scisignal.2001966
GSEA is a statistical functional enrichment analysis commonly applied to ... the probability (P value) of observing measurements in that range (Slide 6).
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39
Simplifying p-value calculation for the unbiased microRNA ...
https://ceur-ws.org/Vol-2841/SIMPLIFY_12.pdf
microRNA enrichment analysis using Machine Learning tech- niques, in order to predict p-values instead of calculating them.
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https://ceur-ws.org/Vol-2841/SIMPLIFY_12.pdf
microRNA enrichment analysis using Machine Learning tech- niques, in order to predict p-values instead of calculating them.
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40
gseResultsSep: A list of separated gene set enrichment p ...
https://rdrr.io/bioc/RTopper/man/gseResultsSep.html
A list containing distinct named numeric vectors corresponding to the gene set enrichment p-value separately computed with runBatchGSE for each distinct ...
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https://rdrr.io/bioc/RTopper/man/gseResultsSep.html
A list containing distinct named numeric vectors corresponding to the gene set enrichment p-value separately computed with runBatchGSE for each distinct ...
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41
List enrichment widgets statistics - InterMine
http://intermine.org/im-docs/docs/webapp/lists/list-widgets/enrichment-widgets
The term can be something like a publication name or a GO term. The count is the number of times that term appears for objects in your list. The p-value is the ...
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http://intermine.org/im-docs/docs/webapp/lists/list-widgets/enrichment-widgets
The term can be something like a publication name or a GO term. The count is the number of times that term appears for objects in your list. The p-value is the ...
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42
GO Enrichment Analysis - Galaxy Training!
https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/tutorial.html
The differentially expressed genes can be identified using the adjusted p-value (also known as FDR). The logFC values indicate whether genes are more expressed ...
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https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/tutorial.html
The differentially expressed genes can be identified using the adjusted p-value (also known as FDR). The logFC values indicate whether genes are more expressed ...
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43
Clustering & Function Enrichment Analysis - Cornell University
https://biohpc.cornell.edu/doc/rna-seq-2020-lecture3.pdf
(Gene Set Enrichment Analysis). Fisher Exact. K-S (Kolmogorov-Smirnov). Statistics. Methods. Input DE gene list. DE gene list + p-values (or score) ...
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https://biohpc.cornell.edu/doc/rna-seq-2020-lecture3.pdf
(Gene Set Enrichment Analysis). Fisher Exact. K-S (Kolmogorov-Smirnov). Statistics. Methods. Input DE gene list. DE gene list + p-values (or score) ...
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44
clusterProfiler 4.0: A universal enrichment tool for interpreting ...
https://www.cell.com/the-innovation/pdf/S2666-6758(21)00066-7.pdf
results using different criteria (e.g., adjusted p values less than 0.001, and the number of input genes annotated to the enriched term ...
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https://www.cell.com/the-innovation/pdf/S2666-6758(21)00066-7.pdf
results using different criteria (e.g., adjusted p values less than 0.001, and the number of input genes annotated to the enriched term ...
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45
8/3/05 1 - Gene Set Enrichment Analysis: A Knowledge-Based ...
https://stat.duke.edu/~sayan/webPub/GSEA_sub.pdf
We estimate the statistical significance (nominal P-value) of the ES, using an empirical phenotype-based permutation test procedure that ...
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https://stat.duke.edu/~sayan/webPub/GSEA_sub.pdf
We estimate the statistical significance (nominal P-value) of the ES, using an empirical phenotype-based permutation test procedure that ...
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46
GO Enrichment Analysis Service - Creative Proteomics
https://www.creative-proteomics.com/services/go-enrichment-analysis-service.htm
P-value is the probability or chance of seeing at least x number of proteins out of the total n proteins in the list annotated to a particular GO term, ...
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https://www.creative-proteomics.com/services/go-enrichment-analysis-service.htm
P-value is the probability or chance of seeing at least x number of proteins out of the total n proteins in the list annotated to a particular GO term, ...
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47
Gene set enrichment analysis: performance evaluation ... - ZLab
https://zlab.umassmed.edu/zlab/publications/Hung_Weng.pdf
performing a t-test and requiring P-value <0.01), and then use a Fisher's exact test to determine whether a significant number of these ...
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https://zlab.umassmed.edu/zlab/publications/Hung_Weng.pdf
performing a t-test and requiring P-value <0.01), and then use a Fisher's exact test to determine whether a significant number of these ...
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48
Bioinformatics analysis reveals different gene expression ...
https://www.spandidos-publications.com/10.3892/etm.2018.6884
All genes in the genome were used as the enrichment background. Terms with a P-value of <0.01, a minimum count of 3 and an enrichment factor ...
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https://www.spandidos-publications.com/10.3892/etm.2018.6884
All genes in the genome were used as the enrichment background. Terms with a P-value of <0.01, a minimum count of 3 and an enrichment factor ...
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49
Separate enrichment analysis of pathways for up - Journals
https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2013.0950
they all calculate the enrichment p-values of pathways for a user-preselected list of interesting genes using slightly different statistical methods, ...
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https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2013.0950
they all calculate the enrichment p-values of pathways for a user-preselected list of interesting genes using slightly different statistical methods, ...
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50
Gene List Enrichment Analysis - Statistics, Tools, Data ...
http://tanlab.org/teaching/CANB7640/LECTURES2018/LECTURE05.pdf
(p- value). • Is List A contains genes involved in List B ... (calculate enrichment p-values with statistical methods). Results.
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http://tanlab.org/teaching/CANB7640/LECTURES2018/LECTURE05.pdf
(p- value). • Is List A contains genes involved in List B ... (calculate enrichment p-values with statistical methods). Results.
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51
Gene Set Enrichment Analysis
https://www.usu.edu/math/jrstevens/stat5570/GSEA_4up.pdf
▫Take the maximal enrichment score for that set. ▫Permute the condition labels to get a null distribution of enrichment scores. ▫Get the p-value by ...
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https://www.usu.edu/math/jrstevens/stat5570/GSEA_4up.pdf
▫Take the maximal enrichment score for that set. ▫Permute the condition labels to get a null distribution of enrichment scores. ▫Get the p-value by ...
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52
Bader Lab @ The University of Toronto
http://baderlab.org/CancerStemCellProject/VeroniqueVoisin/AdditionalResources/GSEA
The nominal p-value estimates the statistical significance of a single gene set's enrichment score, based on the permutation-generated null ...
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http://baderlab.org/CancerStemCellProject/VeroniqueVoisin/AdditionalResources/GSEA
The nominal p-value estimates the statistical significance of a single gene set's enrichment score, based on the permutation-generated null ...
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53
Compute enrichment of gene sets in our predictions #6 - GitHub
https://github.com/Murali-group/SARS-CoV-2-network-analysis/issues/6
There are two approaches I suggest: For every top-k predictions, use Fisher's exact test (hypergeometric test) to compute the p-value of the intersection of the ...
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https://github.com/Murali-group/SARS-CoV-2-network-analysis/issues/6
There are two approaches I suggest: For every top-k predictions, use Fisher's exact test (hypergeometric test) to compute the p-value of the intersection of the ...
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54
Gene set enrichment analysis - CLC Manuals - clcsupport.com
https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Gene_set_enrichment_analysis.html
The permutation based p-value is the number of permutation based test statistics above (or below) the value of the test statistic for the original data, divided ...
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https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Gene_set_enrichment_analysis.html
The permutation based p-value is the number of permutation based test statistics above (or below) the value of the test statistic for the original data, divided ...
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55
Visualization of Functional Enrichment Result
https://bioc.ism.ac.jp/packages/3.7/bioc/vignettes/enrichplot/inst/doc/enrichplot.html
Bar plot is the most widely used method to visualize enriched terms. It depicts the enrichment scores (e.g. p values) and gene count or ...
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https://bioc.ism.ac.jp/packages/3.7/bioc/vignettes/enrichplot/inst/doc/enrichplot.html
Bar plot is the most widely used method to visualize enriched terms. It depicts the enrichment scores (e.g. p values) and gene count or ...
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56
Advanced high-throughput enrichment analysis - GeneTrail
https://genetrail.bioinf.uni-sb.de/help?topic=workflow_geneTrail2
Multiple testing procedures adjust p-values derived from multiple statistical tests to correct for the number of false positive predictions (Type-I-Error). See ...
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https://genetrail.bioinf.uni-sb.de/help?topic=workflow_geneTrail2
Multiple testing procedures adjust p-values derived from multiple statistical tests to correct for the number of false positive predictions (Type-I-Error). See ...
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57
A Bayesian extension of the hypergeometric test for functional ...
https://labordoc.ilo.org/discovery/fulldisplay/cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3954234/41ILO_INST:41ILO_V1
The hypergeometric P-value has been widely used to investigate whether genes from pre-defined functional terms, for example, Gene Ontology (GO), are enriched in ...
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https://labordoc.ilo.org/discovery/fulldisplay/cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3954234/41ILO_INST:41ILO_V1
The hypergeometric P-value has been widely used to investigate whether genes from pre-defined functional terms, for example, Gene Ontology (GO), are enriched in ...
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58
Enrichment Analysis
http://www.cs.tau.ac.il/~rshamir/abdbm/pres/17/Enrichment.pdf
the enrichment p-value. • For a given target set Tj, sample many random gene sets of the same size; compute their p-values vs. each of the terms Ai.
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http://www.cs.tau.ac.il/~rshamir/abdbm/pres/17/Enrichment.pdf
the enrichment p-value. • For a given target set Tj, sample many random gene sets of the same size; compute their p-values vs. each of the terms Ai.
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59
Visualization of Functional Enrichment Result - TU Dortmund
https://bioconductor.statistik.tu-dortmund.de/packages/3.8/bioc/vignettes/enrichplot/inst/doc/enrichplot.html
Bar plot is the most widely used method to visualize enriched terms. It depicts the enrichment scores (e.g. p values) and gene count or ratio as bar height and ...
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https://bioconductor.statistik.tu-dortmund.de/packages/3.8/bioc/vignettes/enrichplot/inst/doc/enrichplot.html
Bar plot is the most widely used method to visualize enriched terms. It depicts the enrichment scores (e.g. p values) and gene count or ratio as bar height and ...
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60
Gene Set Enrichment Analysis Made Simple
https://biostats.bepress.com/jhubiostat/paper185/
A common statistical approach is to quantify the interest of each gene with a p-value, adjust these p-values for multiple comparisons, chose an appropriate ...
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https://biostats.bepress.com/jhubiostat/paper185/
A common statistical approach is to quantify the interest of each gene with a p-value, adjust these p-values for multiple comparisons, chose an appropriate ...
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61
Gene set enrichment analysis - BITS wiki
https://wiki.bits.vib.be/index.php/Gene_set_enrichment_analysis
This requirement for an arbitrarily user-defined threshold (for example, genes with p-value >0.01 are called not-significant) causes an loss ...
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https://wiki.bits.vib.be/index.php/Gene_set_enrichment_analysis
This requirement for an arbitrarily user-defined threshold (for example, genes with p-value >0.01 are called not-significant) causes an loss ...
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62
Gene-set enrichment analysis with topGO (part-1) - DataCATz
https://datacatz.wordpress.com/2018/01/19/gene-set-enrichment-analysis-with-topgo-part-1/
Genes are ordered according to a meaningful metric (eg: fold change, p-value, absolute t-static etc.) and no arbitrary threshold is required ...
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https://datacatz.wordpress.com/2018/01/19/gene-set-enrichment-analysis-with-topgo-part-1/
Genes are ordered according to a meaningful metric (eg: fold change, p-value, absolute t-static etc.) and no arbitrary threshold is required ...
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63
Gene Ontology (GO) Term Enrichment using PANTHER ... - TAIR
https://www.arabidopsis.org/download_files/Help_Documents/PANTHERTermEnrichmentHelp.pdf
the single-test P-value by the number of independent tests to obtain an expected error rate. How to Perform a Basic Term Enrichment Analysis.
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https://www.arabidopsis.org/download_files/Help_Documents/PANTHERTermEnrichmentHelp.pdf
the single-test P-value by the number of independent tests to obtain an expected error rate. How to Perform a Basic Term Enrichment Analysis.
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64
Ontologies and Enrichment
http://sbc.shef.ac.uk/rnaseq-introduction-online/03-enrichment.nb.html
... and people often use quite relaxed criteria for identifying DE genes (e.g. raw rather than adjusted p-values or FDR value).
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http://sbc.shef.ac.uk/rnaseq-introduction-online/03-enrichment.nb.html
... and people often use quite relaxed criteria for identifying DE genes (e.g. raw rather than adjusted p-values or FDR value).
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65
Gene Set Enrichment (4:19) - Module 4 | Coursera
https://www.coursera.org/lecture/statistical-genomics/gene-set-enrichment-4-19-7mvez
Alternatively you can take the smallest p value to the largest p value. And so over here are the most statistically significant associations and over here ...
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https://www.coursera.org/lecture/statistical-genomics/gene-set-enrichment-4-19-7mvez
Alternatively you can take the smallest p value to the largest p value. And so over here are the most statistically significant associations and over here ...
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66
Gene set enrichment analysis: A knowledge-based approach ...
https://www.cs.tufts.edu/comp/167/gsea.pdf
Again, approximate P values can be estimated by permutation of genes. An Initial Catalog of Human Gene Sets. GSEA evaluates a query microarray data set by using ...
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https://www.cs.tufts.edu/comp/167/gsea.pdf
Again, approximate P values can be estimated by permutation of genes. An Initial Catalog of Human Gene Sets. GSEA evaluates a query microarray data set by using ...
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67
Independent Enrichment Analysis - Appyters
https://appyters.maayanlab.cloud/Independent_Enrichment_Analysis/a8db17bcc779d98ca377f653c7b4c0f85f22d741/
The Appyter performs the Fisher exact test to compute enrichment p-value and q-values, and reports the results as a sorted table, a bar graph, ...
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https://appyters.maayanlab.cloud/Independent_Enrichment_Analysis/a8db17bcc779d98ca377f653c7b4c0f85f22d741/
The Appyter performs the Fisher exact test to compute enrichment p-value and q-values, and reports the results as a sorted table, a bar graph, ...
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68
An Overview of Gene Set Enrichment Analysis - UCLA Statistics
http://www.stat.ucla.edu/~jingyi.li/statsm254-s14/survey_papers/ChelseaJU.pdf
Additional Key Words and Phrases: Microarray, Genomic, Enrichment Analysis ... The p-value is described by the fraction of gene set statistics in the re- ...
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http://www.stat.ucla.edu/~jingyi.li/statsm254-s14/survey_papers/ChelseaJU.pdf
Additional Key Words and Phrases: Microarray, Genomic, Enrichment Analysis ... The p-value is described by the fraction of gene set statistics in the re- ...
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69
Enrichment analysis - TargetMine - Mizuguchi Lab
https://targetmine.mizuguchilab.org/documentation/enrichment-analysis/
An example of enrichment widgets. There are four values needed for calculating the p-value. The number of how many genes (or proteins) in the whole genome ...
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https://targetmine.mizuguchilab.org/documentation/enrichment-analysis/
An example of enrichment widgets. There are four values needed for calculating the p-value. The number of how many genes (or proteins) in the whole genome ...
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70
fgsea: Fast Gene Set Enrichment Analysis
https://bioconductor.unipi.it/packages/3.15/bioc/manuals/fgsea/man/fgsea.pdf
Gene-level statistic values used for ranking, the same as in 'fgsea()'. pval.threshold Two pathways are considered dependent when p-value of enrichment of ...
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https://bioconductor.unipi.it/packages/3.15/bioc/manuals/fgsea/man/fgsea.pdf
Gene-level statistic values used for ranking, the same as in 'fgsea()'. pval.threshold Two pathways are considered dependent when p-value of enrichment of ...
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71
Gene Set Enrichment Analysis - ScholarWorks @ GSU
https://scholarworks.gsu.edu/cgi/viewcontent.cgi?referer=&httpsredir=1&article=1080&context=math_theses
the P-values of the genes in the gene set (Pavlidis, et al., 2004). A group of very different approaches starts the analysis from the raw expression data.
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https://scholarworks.gsu.edu/cgi/viewcontent.cgi?referer=&httpsredir=1&article=1080&context=math_theses
the P-values of the genes in the gene set (Pavlidis, et al., 2004). A group of very different approaches starts the analysis from the raw expression data.
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72
GO Enrichment - Bioinformatics Team (BioITeam) at the ...
https://wikis.utexas.edu/display/bioiteam/GO+Enrichment
In this lab, we'll look at how to identify enriched gene ontology (GO) ... INPUT FILE: ALLRANKED (all genes, ranked by adjusted pvalue).
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https://wikis.utexas.edu/display/bioiteam/GO+Enrichment
In this lab, we'll look at how to identify enriched gene ontology (GO) ... INPUT FILE: ALLRANKED (all genes, ranked by adjusted pvalue).
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73
GOnet help - DICE Tools
https://tools.dice-database.org/GOnet/doc/enrich_bg
Computing GO enrichment p-values ... A p-value is computed as a survival function of hypergeometric distribution with shape parameters (M, n, N) at point x. Index ...
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https://tools.dice-database.org/GOnet/doc/enrich_bg
Computing GO enrichment p-values ... A p-value is computed as a survival function of hypergeometric distribution with shape parameters (M, n, N) at point x. Index ...
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74
How GO::TermFinder calculates P-values
https://go.princeton.edu/GOTermFinder/GOTermFinder_calculatePvalues.html
The corrected p-value is calculated as the fraction of simulations having any p-value as good or better than the observed p-value. Comparison of simulation ...
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https://go.princeton.edu/GOTermFinder/GOTermFinder_calculatePvalues.html
The corrected p-value is calculated as the fraction of simulations having any p-value as good or better than the observed p-value. Comparison of simulation ...
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75
Seurat - Guided Clustering Tutorial - Satija Lab
https://satijalab.org/seurat/articles/pbmc3k_tutorial.html
'Significant' PCs will show a strong enrichment of features with low p-values (solid curve above the dashed line).
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https://satijalab.org/seurat/articles/pbmc3k_tutorial.html
'Significant' PCs will show a strong enrichment of features with low p-values (solid curve above the dashed line).
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76
STRING: functional protein association networks
https://string-db.org/
Welcome to STRING. Protein-Protein Interaction Networks Functional Enrichment Analysis. Organisms 14094; Proteins 67.6 mio; Interactions
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https://string-db.org/
Welcome to STRING. Protein-Protein Interaction Networks Functional Enrichment Analysis. Organisms 14094; Proteins 67.6 mio; Interactions
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77
MetaboAnalyst 5.0
https://www.metaboanalyst.ca/MetaboAnalyst/ModuleView.xhtml
Feature view (Biomarker Module) (09/26/2022);; Enhanced enrichment analysis using ... It currently supports several meta-analysis methods based on p-value ...
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https://www.metaboanalyst.ca/MetaboAnalyst/ModuleView.xhtml
Feature view (Biomarker Module) (09/26/2022);; Enhanced enrichment analysis using ... It currently supports several meta-analysis methods based on p-value ...
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78
Stage- and Subfield-Associated Hippocampal miRNA ... - MDPI
https://www.mdpi.com/2227-9059/10/12/3012
... the parent-child-intersection (pci) method was used for enrichment analysis, ... with a p value < 0.01 and an adjusted p value < 0.01.
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https://www.mdpi.com/2227-9059/10/12/3012
... the parent-child-intersection (pci) method was used for enrichment analysis, ... with a p value < 0.01 and an adjusted p value < 0.01.
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79
System biology approaches identified novel biomarkers and ...
https://portlandpress.com/bioscirep/article/42/11/BSR20221108/232002/System-biology-approaches-identified-novel
Molecular enrichment of its common source will give a disease-modifying ... Based on the number of genes and a P-value of less than 0.05, ...
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https://portlandpress.com/bioscirep/article/42/11/BSR20221108/232002/System-biology-approaches-identified-novel
Molecular enrichment of its common source will give a disease-modifying ... Based on the number of genes and a P-value of less than 0.05, ...
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80
Archive ouverte HAL
https://hal.archives-ouvertes.fr/hal-03854013/document
Priscila P. Zenatti2, Tiago Soares1, Mafalda R. de Matos1, Juliana Ronchi ... enrichment in these two subtypes within IL7R mutant human.
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https://hal.archives-ouvertes.fr/hal-03854013/document
Priscila P. Zenatti2, Tiago Soares1, Mafalda R. de Matos1, Juliana Ronchi ... enrichment in these two subtypes within IL7R mutant human.
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81
Unveiling sex-based differences in Parkinson's disease
https://link.springer.com/article/10.1186/s13293-022-00477-5
P-values were corrected using the Benjamini–Hochberg procedure [31] and ... The total number of edges was examined, and PPI enrichment was ...
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https://link.springer.com/article/10.1186/s13293-022-00477-5
P-values were corrected using the Benjamini–Hochberg procedure [31] and ... The total number of edges was examined, and PPI enrichment was ...
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82
Expansion and Intensification of the North American Monsoon ...
https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2022AV000757
We interpret the enrichment of δDp in the Pliocene relative to late Pleistocene values as reflecting a greater proportion of convective summer ...
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https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2022AV000757
We interpret the enrichment of δDp in the Pliocene relative to late Pleistocene values as reflecting a greater proportion of convective summer ...
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83
Variations in germination and grain quality within a rust ...
https://pubag.nal.usda.gov/download/47837/PDF
While the effect of CO2 enrichment on plant ... P-value. 0.041. 0.065 (NS). Means with the same letter within a parameter and entry are.
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https://pubag.nal.usda.gov/download/47837/PDF
While the effect of CO2 enrichment on plant ... P-value. 0.041. 0.065 (NS). Means with the same letter within a parameter and entry are.
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84
Triptolide in the treatment of membranous nephropathy | DDDT
https://www.dovepress.com/integrated-network-pharmacology-analysis-and-experimental-validation-2-peer-reviewed-fulltext-article-DDDT
Based on enrichment analysis, signaling pathways such as PI3K/AKT, MAKP, ... The top 25 enriched KEGG pathways based on the P value were ...
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https://www.dovepress.com/integrated-network-pharmacology-analysis-and-experimental-validation-2-peer-reviewed-fulltext-article-DDDT
Based on enrichment analysis, signaling pathways such as PI3K/AKT, MAKP, ... The top 25 enriched KEGG pathways based on the P value were ...
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85
Gene List Enrichment Analysis - BaRC
http://barc.wi.mit.edu/education/hot_topics/enrichment/Gene_list_enrichment_Mar10.pdf
What identifiers to use? • Most common method: Get a list of differentially expressed genes. – P value and/or fold change?
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http://barc.wi.mit.edu/education/hot_topics/enrichment/Gene_list_enrichment_Mar10.pdf
What identifiers to use? • Most common method: Get a list of differentially expressed genes. – P value and/or fold change?
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86
Auc function in r. E©GãlÉöH;n|â‰xDÍK
https://www.sweethomeimmobiliare.com/jmgs/auc-function-in-r.html
tapestry Objective To explore the value of routine pulmonary function ... Compute Area Under the Curve (AUC) using the trapezoidal rule. precision = p (r), ...
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https://www.sweethomeimmobiliare.com/jmgs/auc-function-in-r.html
tapestry Objective To explore the value of routine pulmonary function ... Compute Area Under the Curve (AUC) using the trapezoidal rule. precision = p (r), ...
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87
CCSF Home | CCSF
https://www.ccsf.edu/
Personal Enrichment. Learn More · Explore. College Highlights. City College Reports First Sign of Enrollment Stabilization. FOR IMMEDIATE RELEASE: November ...
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https://www.ccsf.edu/
Personal Enrichment. Learn More · Explore. College Highlights. City College Reports First Sign of Enrollment Stabilization. FOR IMMEDIATE RELEASE: November ...
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88
Mineralocorticoid Receptor Pathway Is a Key Mediator of Carf...
https://journals.lww.com/hemasphere/Fulltext/2022/11000/Mineralocorticoid_Receptor_Pathway_Is_a_Key.4.aspx
A P-value of <0.05 was considered statistically significant. ... Pathway enrichment analysis of the statistically significant or differentially expressed ...
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https://journals.lww.com/hemasphere/Fulltext/2022/11000/Mineralocorticoid_Receptor_Pathway_Is_a_Key.4.aspx
A P-value of <0.05 was considered statistically significant. ... Pathway enrichment analysis of the statistically significant or differentially expressed ...
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89
KEGG PATHWAY Database
https://www.genome.jp/kegg/pathway.html
› kegg › pathway
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https://www.genome.jp/kegg/pathway.html
› kegg › pathway
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90
IXL | Math, Language Arts, Science, Social Studies, and Spanish
https://www.ixl.com/
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https://www.ixl.com/
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91
Comprehensive proteomic and metabolomic analysis uncover ...
https://peerj.com/articles/14312/
The P values and false discovery rate (FDR) values (based on multiple hypothesis testing) of the enrichment degree from differential ...
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https://peerj.com/articles/14312/
The P values and false discovery rate (FDR) values (based on multiple hypothesis testing) of the enrichment degree from differential ...
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92
19e6 cutoff scores by afsc - three-dimensions
https://three-dimensions.de/19e6-cutoff-scores-by-afsc.html
Apr 21, 2011 · A cutoff value of < 1. com Waps cutoff scores by afsc 2020. ... health careNormalized Enrichment Score (NES), FDR and nominal p-value were ...
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https://three-dimensions.de/19e6-cutoff-scores-by-afsc.html
Apr 21, 2011 · A cutoff value of < 1. com Waps cutoff scores by afsc 2020. ... health careNormalized Enrichment Score (NES), FDR and nominal p-value were ...
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93
eLife: Latest research
https://elifesciences.org/
Global hypo-methylation in a proportion of glioblastoma enriched for an ... Ants are subjected to logarithmic value perception, causing deviation from pure ...
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https://elifesciences.org/
Global hypo-methylation in a proportion of glioblastoma enriched for an ... Ants are subjected to logarithmic value perception, causing deviation from pure ...
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