false discovery rate fdr
Elevated α-defensin levels in plasma and bronchoalveolar lavage fluid from patients with myositis-associated interstitial lung disease
... All values are expressed as the median and inter-quartile range (IQR). Differences between groups were compared using Mann-Whitney U tests. Differences among groups were determined using the Kruskal–Wallis test for ...
8
DNA methylation and smoking in Korean adults: epigenome-wide association study
... We used methylation β values because they are more easily interpretable as methylation changes than M values [41]—the log2 ratio of methylated probe intensity and unmethylated probe intensity. To identify smoking- ...
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Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC
... the discovery phase of ...both discovery and validation sets were selected for further evaluation by Cox ...by false discovery rate (FDR) method was used if ...
11
Protein network analysis reveals selectively vulnerable regions and biological processes in FTD
... enrichment analysis (SEA). ABAEnrichment performs ontol- ogy gene set enrichment analyses for 26 brain regions ranging in age from 8 postconception weeks to 40 years old from the BrainSpan data set distributed by the ...
13
A new FST method to uncover local adaptation using environmental variables
... Figure 2: False Discovery Rate FDR against significance threshold α for three scenarios IM: Island model, SS: Stepping-Stone model and HS: Hierarchically Structured model and monogenic/p[r] ...
21
Thinking BIG rheumatology: how to make functional genomics data work for you
... Once the identities of the comparison samples are chosen, one should consider including replicates when- ever possible. The statistical power of high-throughput sequencing assays is relatively insensitive to the ...
13
Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome
... Similar to MetaCore, the rationale of implementing the HGC is also for prioritizing candidate genes on the basis of their functional relevance to autoimmune phenotypes. In this case however, candidate genes were chosen ...
11
TCC GUI: a Shiny based application for differential expression analysis of RNA Seq count data
... 10% false discovery rate (FDR), are colored in dark red by default, both the cut-off value and color may be changed by the user (see Step 3 in Additional file ...
6
Synovial fluid biomarkers associated with osteoarthritis severity reflect macrophage and neutrophil related inflammation
... and false discovery rate (FDR) correction was used to assess associations of SF RBM biomarkers with etarfolatide imaging scores reflecting synovial inflammation; radiographic knee OA severity ...
9
Transcriptome sequencing reveals altered long intergenic non coding RNAs in lung cancer
... resulting in 34,308 unique transcripts spanning 14,091 gene loci. Gene expression FPKM values were calculated with Cufflinks v2.0.2 using this custom lncRNA annota- tion file. Additionally, a table comprising read counts ...
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miR-363-5p as potential prognostic marker for hepatocellular carcinoma indicated by weighted co-expression network analysis of miRNAs and mRNA
... Furthermore, before GO enrichment analysis of miRNA targets, target genes of miRNAs in the modules were predicted based on the information in TargetScan (http://www.targetscan.org/), miRanda (http://www.mi- ...
9
Shared facial emotion processing functional network findings in medication naïve major depressive disorder and healthy individuals: detection by sICA
... Two investigators (Xu and Li) visually inspected each IC to separate artifacts from FNs. Our diagnostic criteria for artifacts were consistent with the criteria used by Allen and colleagues [38]. ICs with peak voxels at ...
11
RNA sequencing-based longitudinal transcriptomic profiling gives novel insights into the disease mechanism of generalized pustular psoriasis
... RNA-seq was performed with each sample, and ap- proximately 80 million reads were generated per sample. Sequencing reads were aligned to the human genome and analyzed as described in the methods. Differentially expressed ...
11
Differentially expressed proteins in positive versus negative HNSCC lymph nodes
... Diaminobenzidine; DTT: Dithiothreitol; E-FABP: Fatty Acid-Binding Protein, Epidermal; EMT: Epithelial-Mesenchymal Transition; FDR: False Discovery Rate; FFPE: Formalin-Fixed, Paraffin-Em[r] ...
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Gene alterations in monocytes are pathogenic factors for immunoglobulin a nephropathy by bioinformatics analysis of microarray data
... genes; FDR: False discovery rate; FI: Functional interaction; FPR2 : Formyl peptide receptor 2; Gd-IgA1: Galactose-deficient immunoglobulin A1; GEO: Gene Expression Omnibus; HBDs: Healthy ...
9
Tumor expression, plasma levels and genetic polymorphisms of the coagulation inhibitor TFPI are associated with clinicopathological parameters and survival in breast cancer, in contrast to the coagulation initiator TF
... Abbrevations asTF: alternatively spliced tissue factor; ANOVA: analysis of variance; ELISA: enzyme-linked immunosorbent assay; FDR: false discovery rate; GOBO: Gene expression based Outc[r] ...
15
A maple syrup extract alters lipid metabolism in obese type 2 diabetic model mice
... a false discov- ery rate (FDR) < ...of FDR in the WAT was set to < ...[18]. FDR was calculated from the p value using the Benjamini and Hochberg method ...with FDR < ...
8
Osteogenic commitment of Wharton’s jelly mesenchymal stromal cells: mechanisms and implications for bioprocess development and clinical application
... CM: Conditioned media; EV: Extracellular vesicle; FDR: False discovery rate; GMP: Good manufacturing practice; ISCT: International Society for Cell and Gene Therapy; MSC: Mesenchymal str[r] ...
11
DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma
... Alu: Alu element; ChIP-seq: Chromatin immunoprecipitation sequencing; dmRE: Differentially methylated RE; EtOH: Alcohol; FDR: False discovery rate; H3K27ac: Histone H3 lysine 27 acetylat[r] ...
13
Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells
... database; FDR: False Discovery Rate; FES: Fold Enrichment Score; GAPDH: Glyceraldehyde-3-phosphate dehydrogenase; GDF15: Growth and Differentiation Factor 15; GFP: Green Fluorescent Protein; ...
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