Tag: FPKM

Characteristics of Amorphophallus konjac as indicated by its genome

Genome assembly and annotation The DNA sequencing data (1119.58 Gb, average 110× coverage) of the A. konjac sample were obtained using the Illumina Hiseq 2500 sequencer. A summary of the sequence data used for the assembly is presented in Table S1. The estimated genome size is 4,512,012,462 bp using 19-mer frequency distribution based…

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Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?

Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)? 0 Hi all, I’m trying to figure out how to compare differential gene expression between samples. I’ve gotten to the first steps of data visualization, and using R and ballgown, I can run plotTranscripts or plotMeans to…

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Is there a need to batch correct FPKM or TPM values for within sample comparison

Is there a need to batch correct FPKM or TPM values for within sample comparison 0 Hi all, Does anyone have any insight or experience into whether FPKM/TPM expression should be corrected for batch effect? I have come to notice that batch correction is mostly applied to raw counts and…

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CPTAC data, download, merge

CPTAC data, download, merge 1 Hey friends I downloaded RNA seq data of CPTAC from GDC portal. I want to merge them as one file. I have my python script and manifest file in the same folder and I am running the following code in the command prompt to merge…

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Pan-Cancer Analysis and Validation of Opioid-Related Receptors Reveals

Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…

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LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2’-O-methylation

Ethics statement All mice procedures in this study were performed under an animal protocol approved by the Institutional Animal Care and Use Committee guidelines of Westlake University. The procedures and protocols for glioma patients were approved by the institutional review board of Beijing Tiantan Hospital. Informed consent was obtained from…

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Can FPKM be used to create bar graphs for DEGs?

Can FPKM be used to create bar graphs for DEGs? 0 Hi, I have an Excel sheet of RNAseq results. The raw data was analyzed by a company and was not available to me. I have three sets of data on this sheet besides the gene names and p-values: Raw…

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Convert FPKM to TPM in R

I’m conducting a meta-analysis over several datasets. I want to combine those datasets and run some machine learning algorithms to predict a target response. Some of those datasets are raw counts, which I can easily convert to TPM with the following code: rpkm <- apply(X = subset(counts_data), MARGIN = 2,…

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ABCB1 and immune genes in breast cancer

Introduction Chemoresistance is a major challenge for breast cancer treatment.1 The mechanisms of chemoresistance are complex because of crosstalk between receptor tyrosine kinases and downstream pathways, deregulation of cell-cycle and apoptosis regulators, and modulation of tumor-infiltrating immune cells.2 The ATP-binding cassette (ABC) superfamily is one of the largest families of…

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duplicates issues when trying to convert long to wide in R

duplicates issues when trying to convert long to wide in R 1 library(dplyr) library(tibble) library(tidyr) df <- test %>% mutate(row_id = model_name) %>% pivot_wider(names_from = gene_symbol, values_from = fpkm) ### Warning message: Values from `fpkm` are not uniquely identified; output will contain list-cols. • Use `values_fn = list` to suppress…

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Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma

Statistical methods Statistical tests, test statistics and P values are indicated where appropriate in the main text. Categorical associations were established using the chi-squared test of independence if n > 5 for all categories and Fisherʼs exact test otherwise. For both tests, the Python package scipy.stats v1.5.3 implementation was used64. Multiple hypothesis corrections…

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Identification of circRNA-miRNA-mRNA network as biomarkers for interstitial cystitis/bladder pain syndrome

Research Paper Advance Articles Shi-Qin Yang1, *, , Liao Peng1, *, , Le-De Lin1, , Yuan-Zhuo Chen1, , Meng-Zhu Liu1, , Chi Zhang1, , Jia-Wei Chen1, , De-Yi Luo1, , 1 Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China * Equal contribution…

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Comparing Expression between Cancer Grades

RNA-Seq: Comparing Expression between Cancer Grades 0 Hi everyone, I am doing a project where I am comparing gene expression between cancer grades. What type of count data should I use? I have used VST in this plot. However, would FPKM be better since it would give more of an…

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FPKM values for DE analysis

FPKM values for DE analysis – Why? 1 Hello everyone! I believe my questions are quite naive, but I am super new to RNA-seq data analysis, so forgive me! I already saw some questions regarding this subject, but I still do not understand it well. I am currently performing (trying…

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MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Introduction After the fusion of the oocyte and sperm, the zygote undergoes a series of cell divisions until it forms a blastocyst before implantation into the uterus. A human blastocyst is formed of a fluid-filled cavity and ∼200 cells that comprise three distinct cell types: the trophectoderm (TE), which gives…

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should I use normalized counts or transformed of normalized counts for RNA-seq association analysis?

should I use normalized counts or transformed of normalized counts for RNA-seq association analysis? 1 Hi, I run differential gene expression with DeSeq2. dds <- DESeq(dds) rld <- rlog(dds, blind=False) vsdata <- vst(dds, blind=FALSE) If my goal is to find association between gene expression (RNA-seq ) and methylation, should I…

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NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

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Combining ComBatseq to remove batch effects and fragment size normalization

Combining ComBatseq to remove batch effects and fragment size normalization 0 In order to use a certain R package, I need fragment size adjusted counts such as TPM or FPKM. However, the raw counts are influenced by batch effects and I want to remove batch effects using ComBatseq. Would it…

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Normal vs Tumor – Kaplan Meier Survival Analysis

Normal vs Tumor – Kaplan Meier Survival Analysis 0 To perform survival analysis for normal vs tumor cancer sample what kind of rna seq data is to used? => unstranded => stranded_first => stranded_second => tpm_unstrand => fpkm_unstrand => fpkm_uq_unstrand Which of these shoud be used and is there any…

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Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

Gene expression atlas in fiber development To uncover the genetic regulation of gene expression in fiber development, we collected 376 diverse G. hirsutum accessions for genome and transcriptome analysis. A total of 13.5 Tb of genome resequencing data were generated, with an average depth of 15.6× (Supplementary Table 1). Accessions were…

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Genes | Free Full-Text | Phylogenomic Analysis of Cytochrome P450 Gene Superfamily and Their Association with Flavonoids Biosynthesis in Peanut (Arachis hypogaea L.)

4.1. The Evolution of AhCYP Superfamily: Diversity and Expansion The CYP gene superfamily, one of the largest in plants, plays a pivotal role in catalyzing a diverse range of reactions involved in growth, development, and secondary metabolite biosynthetic pathways. Systematic identification and study of the CYP gene superfamily are paramount….

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Apoptotic stress causes mtDNA release during senescence and drives the SASP

Cell culture and treatments Human embryonic lung MRC5 fibroblasts (ATCC) and IMR90 fibroblasts (ATCC) were grown in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D5796) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U ml−1 penicillin, 100 μg ml−1 streptomycin and 2 mM l-glutamine and maintained at 37 °C under 5% CO2. MRC5 fibroblasts were cultured in…

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Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma

Study approval and patient consent The study protocol was approved by the Ethics Committee of Qinghai Provincial People’s Hospital (approval number: 2023-141) and conducted in accordance with the ethical principles for medical research involving human subjects described in the Declaration of Helsinki in addition to relevant Chinese laws and institutional…

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RNA sequencing and gene expression analysis in a Mouse model

Introduction Chronic obstructive pulmonary disease (COPD) is a condition that is characterized by persistent respiratory symptoms and airflow limitations that are not fully reversible. The severe complications of the disease may adversely affect its morbidity and mortality.1 According to World Health Organization (WHO) statistics, over 3 million people per year…

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TRIM25 targets p300 for degradation

Introduction Protein levels are regulated at several nodes. One mode of protein level regulation acts through enhancing or reducing gene transcription. Gene transcription can be stimulated by binding transcription factors to promoters or enhancers of target genes and by posttranslational modifications of transcription factors and histones. Such modifications can be…

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Calculating TPM from featureCounts output

Calculating TPM from featureCounts output 3 Hi all, Have a simple question but just want to double check I’m not doing something stupid. I have paired-end RNA-seq data for which I have used featureCounts to quantify raw counts. I now want to normalize using the TPM formula. I read this…

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Is it possible to convert 3 prime sequencing read counts into TPMs?

Is it possible to convert 3 prime sequencing read counts into TPMs? 1 I have got read counts from 3 prime sequencing and would like to make a rough comparison with other RNAseq dataset for which have got transcripts per million (TPM) values. Is it possible to convert the read…

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High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis

Introduction Single-cell RNA sequencing (RNA-seq) was first achieved by using a quantitative cDNA amplification method and applied to mouse oocytes (Kurimoto et al, 2006; Tang et al, 2009). It has since provided unprecedented opportunities for the study of cellular differentiations, states, and diseases in various biological fields, including developmental biology,…

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Bioconductor – Linnorm

DOI: 10.18129/B9.bioc.Linnorm   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Linnorm. Linear model and normality based normalization and transformation method (Linnorm) Bioconductor version: 3.16 Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large…

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Bioconductor – zFPKM

DOI: 10.18129/B9.bioc.zFPKM   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see zFPKM. A suite of functions to facilitate zFPKM transformations Bioconductor version: 3.16 Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013…

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Genome-wide identification of lncRNA & mRNA for T2DM

Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi Arabia Correspondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email [email protected] Purpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with…

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PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset

PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset 4 Hi, I am wondering in which normalisation format (RPKM, FPKM, TPM,… etc) the PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset (the EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv file available here) is in? I know it is batch-corrected, but I don’t know in which normalisation format the original data was in. Thanks…

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A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae

A Ct strain severely inhibits plant growth in a nutrient-dependent manner A Ct strain, Ct61, isolated from a wild A. thaliana population in Spain, promotes plant growth under low Pi conditions by transferring phosphorus to the host3. In addition to Ct61, five different Ct strains have been isolated from various…

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Cancers | Free Full-Text | CPSF3 Promotes Pre-mRNA Splicing and Prevents CircRNA Cyclization in Hepatocellular Carcinoma

The real effect of CPSF3 on circRNA expression in HCC cells was tested by analyzing the total RNA fractions obtained from CPSF3-KO HepG2 cells, CPSF3-OE Bel7404 cells, and negative control cells using high-throughput sequencing (Supplementary Files S7 and S8). The data obtained showed that CPSF3-KO cells had more types and…

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Low-dose radiation induces unstable gene expression in developing human iPSC-derived retinal ganglion organoids

RGCs from human iPSCs for genomic analysis We developed neuronal organoids, including RGCs from human iPSCs, to assess the effects of low-dose irradiation. Phase-contrast microscopy (Supple Fig. S1a) indicated time-dependent morphological changes in the embryonal body formed from human iPSCs, which corresponded to previous reports14, 15. Retinal development was evaluated…

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Unsupervised clustering on gene expression data

Clustering is a data mining method to identify unknown possible groups of items solely based on intrinsic features and no external variables. Basically, clustering includes four steps: 1) Data preparation and Feature selection, 2) Dissimilarity matrix calculation, 3) applying clustering algorithms, 4) Assessing cluster assignment I use an RNA-seq dataset…

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Calculating FPKM and TPM by hand from htseq-count output?

Calculating FPKM and TPM by hand from htseq-count output? 0 Hello! I am counting reads with htseq-count, and wasted some hours trying to find an extant software that would calculate FPKM and/or TPM from that output, so I wrote a script myself. There is just one question mark – should…

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Collecting columns from multiple files into one file

Collecting columns from multiple files into one file 1 Dear all, I hope you are all doing well. I’m new to bioinformatics and would be grateful if you could help me with the below issue. I have 156 files named with sample_1_TEcounts.tsv, sample_2_TEcounts.tsv, … and contain information as in the…

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Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes

Sample collection, library construction and sequencing Leaves of two diploid C. paliurus (PG-dip and PA-dip) and one auto-tetraploid (PA-tetra) for genome sequencing were collected from plants grown in germplasm bank of C. paliurus, which located in Baima experimental field, Nanjing, Jiangsu province, China. After collecting, tissues were immediately frozen in…

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Identification of bromelain subfamily proteases encoded in the pineapple genome

C1A protease family genes in the pineapple MD2 v2 genome Presence of either the C1 peptidase or I29 inhibitor domains were used as a signature to identify genes belonging to the C1A protease gene family9. 71 C1A genes were identified (AcC1A1–AcC1A71), and were distributed across 17 pineapple chromosomes (Fig. 1,…

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Revisit where to find CCLE RNAseq in FPKM or RPKM using RSEM values to perform normalization- as was never answered usefully

Revisit where to find CCLE RNAseq in FPKM or RPKM using RSEM values to perform normalization- as was never answered usefully 0 I would like to find the CCLE RNA expression file that has either effective gene sizes or FPKM /RPKM (where estimated RSEM values have been used) to do…

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RNAseq RAW DATA of bacterial interactions with avocado roots

RNAseq comparing wt strain PcPCL1606 and the derivative mutant AdarB, defective in HPR production. RNA was extracted from the rhizosphere samples using a PowerSoil® RNA extraction kit (Qiagen Iberia S.L., Madrid, Spain) following the manufacturer’s instructions and its amount was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham,…

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Plotting ATAC-seq data over RNA-seq?

Plotting ATAC-seq data over RNA-seq? 0 Hi everyone, I am new to this space and have no bioinformatics background — with very limited knowledge on data processing. So I apologize ahead of time if any of my questions are extremely stupid or make no sense 🙂 I did manage to…

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cBioPortal data with negative log2(FPKM + 1) values

cBioPortal data with negative log2(FPKM + 1) values 0 Hello, I am looking at data downloaded from cBioPortal directly. The metadata for the mrna-seq files asserts the data are log2(FPKM + 1), but there values as small as -0.3 in the matrix. I am thinking maybe they did log2(FPKM) +…

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Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival

Characterization of genomic landscape We compared somatic variants, copy number alterations, and mutational burden between the primary and metastatic tumors of the ST and LT survival groups. Our cohort of patient tumors exhibited characteristics typical of those seen in previously sequenced HGSC tumors, such as nearly ubiquitous TP53 mutations, high…

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Importing RSEM processed data already formatted as a summarized experiment into DESeq2

Hello, I have a fairly simple question that I know has been addressed many times: I want to import RSEM data into DESeq2 for modeling and DE. For reproducibility, the workflow is: Unfortunately, it is costing me an inordinate amount of time, and I cannot find a perfectly analogous example…

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Construction & ID of an NLRs-associated Prognostic Signature

Introduction Skin cutaneous melanoma (SKCM) is the most severe dermatologic malignancy, and its incidence has increased worldwide in recent years.1 SKCM accounts for 1% of all skin cancer patients, yet it is responsible for roughly 80% of all skin cancer deaths.2 Early-stage SKCM (localized or regional) can be surgically removed,…

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Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Timecourse of Hox gene activation in stembryos In gastrulating mouse embryos, Wnt signaling contributes to the formation of the primitive streak from epiblast cells. Likewise, in stembryos cultured as described in ref. 34, a pulse of the Wnt agonist Chiron 48 h after aggregation of mES cells, that is, between 48 h…

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Bioconductor EDIRquery

Comment: DESeq2 remove batch effect by James W. MacDonald 63k I would reverse 1 and 2 Answer: Fishpond with unbalanced dataset by Michael Love 40k Thanks for the report, I will follow up on GH. Answer: Can DESeq2 handle low number of samples and replicates? by Michael Love 40k There…

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Appropriate RPKM cutoff

Appropriate RPKM cutoff 0 Hey, I’m using multiple previously published RNA-Seq studies as validation and to search for similar “signatures” as in our data. For these other studies I have their final read counts, and statistically significant filtered data that includes RPKM, FPKM, or other normalized read values as per…

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What Are The Most Common Stupid Mistakes In Bioinformatics?

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

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A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology

Statement on ethical considerations All animal work was approved and permitted by the Local Ethical Committee on Animal Experiments and conducted according to the Guidelines for Animal Experimentation recommendations (ARRIVE guidelines). In particular, mouse work related to C57BL/6NCrl mice was approved and permitted by the Institute of Molecular Genetics of…

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Genes’ fpkm values through cufflink

Hi, I am a newbie to RNA-seq data analysis. I have to identify differentially expressed genes (DEGs) between human and chimpanzee in a tissue type. I have comparable RNA-seq experiment data (reads/fastq) for the two species. Each species has 2 biological replicates(each with three technical replicates) so six runs per…

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BED file showing an error while performing the FPKM count in Galaxy Europe

BED file showing an error while performing the FPKM count in Galaxy Europe 0 When I’m running FPKM Count program in the Galaxy Europe website i’m getting an error which is a s follows: [W::hts_idx_load3] The index file is older than the data file: input.bam.bai Extract exon regions from /data/dnb08/galaxy_db/files/f/b/4/dataset_fb483fc1-0b18-4aa6-aa5c-c2b9fd8047da.dat……

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Scientists identify mutated gene behind mirror movement disorder

Arhgef7 is required for Netrin-1–mediated commissural axon guidance. (A) The mean mRNA expression, fragments per kilobase of transcript per million mapped reads (fpkm), (± SEM) of Arhgef7 and Dcc in dissociated commissural neurons (n = 3). (B) Dissociated commissural neurons were fixed and immunostained for Arhgef7 and Dcc. Scale bar,…

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Obtaining TPM values from STAR alignment and counts with featurecounts using R’s tidyverse syntax (dplyr and tidyr)

Hello! I have a table of counts that I got by aligning rna seq samples with STAR and using featureCounts, and my goal is to get TPM values for each gene of the table. As a first step, I imported my table into R and modified it a bit to…

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Count Matrix normalisation for downstream analysis and for creating heatmap of targeted genes

Count Matrix normalisation for downstream analysis and for creating heatmap of targeted genes 0 Hello Everyone! I have a count matrix generated from stringtie (from FPKM to readcount using prepDE.py3 of stringtie). i would like to create heatmap of targeted genes across samples. My questions are : 1) Before creating…

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Muscle RNAseq data implicates interferon-beta in dermatomyositis

Muscle RNAseq data implicates interferon-beta in dermatomyositis (A) Selective elevation of interferon-beta (IFNB) 1 among other type 1 interferons in dermatomyositis muscle.(B) Specificity of IFNB1 elevation in dermatomyositis compared with other inflammatory myopathies and healthy muscle. RNAseq: RNA sequencing; DM: dermatomyositis; FPKM: fragments per kilobase of exon model per million reads…

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Highly-conserved regulatory activity of the ANR family in the virulence of diarrheagenic bacteria through interaction with master and global regulators

ANR is relatively conserved among diarrheagenic pathogens Over the last 5 years, massive sequencing of new bacterial genomes has identified hundreds of new ANR members in multiple pathogens. ANR is widely distributed in at least 26 Gram-negative bacterial species29,31. Phylogenetic analysis of the amino acid sequence of ANR members from clinically…

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Gene Expression Analysis c Flashcards

What is used to measure transcript abundance? a variety of units, which have different requirements in order to ensure comparisons are meaningful number of reads that align to a given feature What unit does differential expression often use? What do counts depend on? sequencing depth/library size and on feature length,…

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How to get TPM / FPKM after batch correction with DESeq2?

How to get TPM / FPKM after batch correction with DESeq2? 1 @cfe7a460 Last seen 40 minutes ago Europe I’m trying to adjust batch effect using deseq2 limma::removeBatchEffect like below: ###### Batch Correction with limma removeBatchEffect ####### dds <- DESeqDataSetFromMatrix(countData = data, colData = coldata, design = ~ Samplebatch +…

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Why Batch effect removal with Combat-seq and DESeq2 give different results?

I’m trying to adjust batch effect using deseq2 limma::removeBatchEffect and also Combat-Seq. With limma version, I can clearly see the batch effect is removed, where I see control from Batch1 is together with the other 3 controls from Batch2. ###### Batch Correction with limma removeBatchEffect ####### dds <- DESeqDataSetFromMatrix(countData =…

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Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome

Ethics statement All animal experimentation was conducted according to the National Institutes of Health guidelines for the housing and care of laboratory animals. All experiments were performed in accordance with institutional regulations after review and approval by the Animal Studies Committee at Washington University School of Medicine in St Louis,…

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PUREE: accurate pan-cancer tumor purity estimation from gene expression data

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

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fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data

Comput Struct Biotechnol J. 2023; 21: 2276–2285. ,a,1 ,a,1 ,a ,b,c and a,b,⁎ Leiming Jiang aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Shijia Hao aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Lirui Lin aComputational…

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How to Merge RNA Replicates

How to Merge RNA Replicates 1 I am following the manual for a program called TimeReg that says “If there are multiple replicates, merge them to get one expression profile. For gene expression data, you may use the average expression (FPKM or TPM) of the replicates.” I have two replicates…

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in an RNA-seq experiment, what threshold would you use to define a set of expressed or active genes in a cell line?

in an RNA-seq experiment, what threshold would you use to define a set of expressed or active genes in a cell line? 0 I am trying to define a set of expressed (active) genes in my cell line for some downstream analysis. What would be your approach for defining this…

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Inactivation of interleukin-30 in colon cancer stem cells via CRISPR/Cas9 genome editing inhibits their oncogenicity and improves host survival

Introduction Colorectal cancer (CRC) is a leading cause of cancer-related death1 and its mortality rate is expected to rise worldwide, due to population growth and aging, thus entailing a global public health challenge. CRC mortality is mainly due to therapy resistance and metastasis, which are driven by a small population…

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Please give me a grep command to get Gene IDS and TPM values from a stringtie output gtf file

Please give me a grep command to get Gene IDS and TPM values from a stringtie output gtf file 2 Hi, Could anyone please give me a grep command to get gene_id and respective TPM values from a string tie output file. My result output file looks like the following…

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samtools idxstats versus samtools view command

samtools idxstats versus samtools view command 1 Hi, I have mapped RNA-seq data to the human genome concatenated with a viral genome (26 chromosomes in total) with bowtie and need to get some numbers to calculate FPKM values manually for one viral gene, to retrieve the “total number of reads”…

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Discrepancy between Log2(x) and Log2(x+1) regarding Log2FC

Often in DE-analysis count values (FPKM or TPM) are log transformed with pseudocounts such as Log2(x+1) or Log2(x+0.1), which is done to avoid negative values. Alas, I have noticed a discrepancy I can’t get my head around. Suppose we have two expression values: 30 and 60. Using normal values, Log2FC…

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KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset

Hello, I am new to bioinformatic analyses and I am trying to analyse the TCGA dataset to plot a survival curve based on the expression of a gene of interest (say TP53). I have written the following code to analyse the TCGA data, but I am unable to proceed further…

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Should I use TPM or TMM to plot gene expression boxplots in RNAseq?

Should I use TPM or TMM to plot gene expression boxplots in RNAseq? 0 Hi all! I used $TRINITY_HOME/util/align_and_estimate_abundance.pl from trinity to do transcript quantification for my RNAseq data. Then I got the following outputs: I would like to plot the boxplots for several genes. Which one should I use….

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I have a question for deg analysis tools

I have a question for deg analysis tools 1 Hi. I’m going to do DEG analysis with tmp data that has already been normalized. I want to use a total of four tools; DESeq2, edgeR, Ballgown, Limma. But I already knew the raw count data can only be used in…

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Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

We aimed to assess the extent to which it was possible to effectively normalize and combine microarray and RNA-seq data with existing methods for use as a training set for machine learning applications. We assessed performance on holdout sets composed entirely of microarray data and entirely of RNA-seq data. To…

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Can FPKM data sets be of any use or are they trash?

Can FPKM data sets be of any use or are they trash? 2 Hello all. I have acquired FPKM-normalized data sets (excel files) which are (supposedly) to be used for differential expression analysis. As is well known, FPKM normalization is not the best strategy in the current day and age….

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Get TPM from RNA counts and gene length?

Get TPM from RNA counts and gene length? 1 Hello, I am working with an RNA-seq FeatureCounts output file that supplies the counts for a given ENSG gene ID, as well as the gene length(according to documentation this is in base pairs, not kilobases). Is there a way to obtain…

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A heterophil/lymphocyte-selected population reveals the phosphatase PTPRJ is associated with immune defense in chickens

Ethics statement and animals All animals and experimental protocols used in this study were approved by the Beijing Institute of Animal Science, Chinese Academy of Agricultural Sciences (the scientific research department responsible for animal welfare issues) (No.: IASCAAS-AE20140615). In this study, experimental chickens (JXH) were selected on H/L, with the…

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A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk

Chromosomal-scale genome assembly and full spidroin gene set of T. clavata To explore dragline silk production in T. clavata, we sought to assemble a high-quality genome of this species. Thus, we first performed a cytogenetic analysis of T. clavata captured from the wild in Dali City, Yunnan Province, China, and…

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Bioinformatics construction and experimental validation of a cuproptosis-related lncRNA prognostic model in lung adenocarcinoma for immunotherapy response prediction

Data collection and processing The RNA-sequencing data, clinical information and simple nucleotide variation of LUAD patients were retrieved from TCGA database (portal.gdc.cancer.gov/, accessed April 8, 2022). Nineteen cuproptosis-related genes (CRG) were mainly collected from previous study, including LIPT1, GLS, NFE2L2, NLRP3, LIAS, ATP7B, ATP7A, SLC31A1, FDX1, LIPT2, DLD, DLAT, PDHA1,…

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Enolase-1 & prognosis & immune infiltration in breast cancer

Introduction Breast cancer is the most prevalent malignancy and the leading cause of cancer death in women worldwide.1 After its diagnosis, the most immediate challenge is to tailor treatment strategies and predict the prognosis; traditional clinicopathologic features, including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2…

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How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression

How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression Why do mRNA expression values need to be normalized? The unification of mRNA expression value measurements across studies, or the normalization of mRNA data, is a significant problem in biomedical and life science research. The abundance of transcripts is measured digitally…

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Comprehensive Analysis of NPSR1-AS1 as a Novel Diagnostic and Prognostic Biomarker Involved in Immune Infiltrates in Lung Adenocarcinoma

The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…

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Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

Software official website : Hisat2: Manual | HISAT2 StringTie:StringTie article :Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial : 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…

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RPKM threshold estimation – SEQanswers

Dear All, I have a doubt in the calculation of False postitive rate while checking for FPKM threshold in a RNAseq experiment. Following the method previously published (www.ploscompbiol.org/article/…l.pcbi.1000598). I am not getting desired results. I followed the method as mentioned the publication Reads were mapped to Ensembl genes (blue) and…

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A hypoxia-related signature in lung squamous cell carcinoma

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

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use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

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Difference of results with the same input [RNAseq analysis]

Difference of results with the same input [RNAseq analysis] 0 Hello! I am trying to optimize the treatment of some RNAseq files by splitting the input reads into several files. I am comparing the results I have obtained with: the reads input as one file the split input as several…

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Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

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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…

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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…

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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…

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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)….

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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…

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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.,…

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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…

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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…

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