Tag: FPKM

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

Continue Reading The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

Continue Reading Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

What is the cutoff used for define high or low expression level of gene for survival analysis

What is the cutoff used for define high or low expression level of gene for survival analysis 1 Hi everyone In RNA-seq analysis, we need to separate samples into two groups for survival analysis. How can I define high level or low level for a gene according to counts or…

Continue Reading What is the cutoff used for define high or low expression level of gene for survival analysis

Using machine learning methods to find a biomarker panel to diagnose a disease.

Hello Biostars. I obtained DEGs from RNAseq analysis for normal and infected samples. Then I decreased the number of them by some downstream analysis. Now I have 120 DEGs and I want to select between them the best combination of biomarkers that can recognize normal from infected samples (biomarker panel)….

Continue Reading Using machine learning methods to find a biomarker panel to diagnose a disease.

How does Cufflinks DE calculate q-value?

How does Cufflinks DE calculate q-value? 5 I have run my aligned samples through the Cufflinks app in Illumina BaseSpace a couple of different ways. When I do Classic FPKM Normalization + Pairwise comparisons, I get a small list of genes. This analysis seems stringent. When I do Classic FPKM…

Continue Reading How does Cufflinks DE calculate q-value?

Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

Continue Reading Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

pre-proccessing of RNAseq data for WGCNA

pre-proccessing of RNAseq data for WGCNA 0 Hi everyone, i wanted to create an expression matrix for WGCNA input. however, i has been said that use RPKM/FPKM data instead of CPM, how can i change my TCGA data to RPKM/FPKM in GDCquery and how to filter expression set of genes…

Continue Reading pre-proccessing of RNAseq data for WGCNA

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis | BMC Genomics

CeTF is an C/C++ implementation in R for PCIT [6] and RIF [7] algorithms, which initially were made in FORTRAN language. From these two algorithms, it was possible to integrate them in order to increase performance and Results. Input data may come from microarray, RNA-seq, or single-cell RNA-seq. The input…

Continue Reading CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis | BMC Genomics