Categories
Tag: MSigDB
Notch signaling in thyrocytes is essential for adult thyroid function and mammalian homeostasis
Brent, G. A. Mechanisms of thyroid hormone action. J. Clin. Invest. 9, 3035–3043 (2012). Article Google Scholar Iwen, K. A., Oelkrug, R. & Brabant, G. Effects of thyroid hormones on thermogenesis and energy partitioning. J. Mol. Endocrinol. 60, R157–R170 (2018). Article PubMed CAS Google Scholar Biondi, B. & Wartofsky, L….
Apoptosis-resistant megakaryocytes produce large and hyperreactive platelets in response to radiation injury | Military Medical Research
Animals C57BL/6-Tg (Pf4-icre) Q3Rsko/J (Pf4-Cre) mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA). B6;129-Tmem173tm1(flox)Smoc (Stingfl) mice were purchased from Shanghai Model Organisms Center, Inc. (Shanghai, China). C57BL/6J-Ifnar1em1(flox)Cya (Ifnar1fl) mice were purchased from Cyagen Biosciences (Guangzhou, China). Stingcko and Ifnar1cko mice were generated by crossing Pf4-Cre mice with…
LncRNA/circRNA-mRNA networks in CARAS | JIR
Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…
Fatty Acid Metabolism-Related lncRNAs as Biomarkers for SKCM
Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…
Deep learning-enabled breast cancer endocrine response determination from H&E staining based on ESR1 signaling activity
Burstein, H. J. Systemic therapy for estrogen receptor-positive, HER2-negative breast cancer. N. Engl. J. Med. 383, 2557–2570. doi.org/10.1056/NEJMra1307118 (2020). Article CAS PubMed Google Scholar Jeselsohn, R. M. The evolving use of SERDs in estrogen receptor-positive, HER2-negative metastatic breast cancer. Clin. Adv. Hematol. Oncol. 19, 428–431 (2021). PubMed Google Scholar McAndrew,…
Unable to connect to the mSigDB database server
I am not able to connect to the mSigDB gene sets database on the Run GSEA tab. I keep getting an error that says it’s timed out and it may be due to firewall rules. But I also tried to connect using my home network which isn’t firewalled and still…
How should I run ssgsea analysis ?
How should I run ssgsea analysis ? 1 I have TPM expression data from RNA-seq data analysis. The data comprises of not only protein coding genes but also several other biotypes like miRNA, lncRNA, pseudogene etc making the matrix genes around 60,000. Here, should I filter by data with biotype=”protein…
Bioinformatics analysis of immune cell infiltration patterns and potential diagnostic markers in atherosclerosis
A database in the Gene Set Enrichment Analysis (GSEA; www.gsea-msigdb.org/gsea/msigdb/index.jsp) platform10,11 was used to identify 134 GLN metabolism-associated genes. Weighted gene co-expression network analysis (WGCNA) and module screening GLN-associated gene sets were investigated using WGCNA. The results demonstrated that when the weighted value was 24 (Fig. 1A), scale independence was greater…
Selecting a subset of MSigDB database for GSEA
Selecting a subset of MSigDB database for GSEA 0 Hi all I am analyzing bulk RNA-seq data with GSEA and MSigDB to identify significantly enriched pathways. I am interested in which signaling pathways are enriched, so I am planning on using “C2: curated gene sets”, its subcollection “CP: Canonical pathways”,…
Index of bioconductor/stats/data-experiment/msigdb/ – SJTUG Mirror Index
bioconductor stats data-experiment msigdb Name Size Modified ../ – – index.html 9.4 kiB 2023-11-11 22:14:32 UTC msigdb_2021_stats.png 23.9 kiB 2023-11-11 22:14:32 UTC msigdb_2021_stats.tab 249 B 2023-11-11 00:15:14 UTC msigdb_2022_stats.png 24.7 kiB 2023-11-11 22:14:32 UTC msigdb_2022_stats.tab 269 B 2023-11-11 10:04:58 UTC msigdb_2023_stats.png 24.7 kiB 2023-11-11 22:14:32 UTC msigdb_2023_stats.tab 264 B 2023-11-11…
error uploading gct file to gsea
error uploading gct file to gsea 0 Hello everyone I’m trying to upload my gct file of the normalized RNAseq counts for mouse into GSEA. I get errors that the last line in my gt file has bad info. I have changed the number of probes in the gct file,…
Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls
World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….
Insights into expression patterns and immunotherapy response prediction
[1] D. Schadendorf, D. E. Fisher, C. Garbe, J. E. Gershenwald, J. Grob, A. Halpern, et al., Melanoma, Nat. Rev. Dis. Primers, 1 (2015), 15003. doi.org/10.1038/nrdp.2015.3 doi: 10.1038/nrdp.2015.3 [2] A. M. M. Eggermont, A. Spatz, C….
Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep
Global changes of the transcriptome during postnatal muscle growth The number of myofibers is thought to remain fixed following birth, muscle fiber hypertrophy growth is the primaryway of muscle growth. The average CSA is generally used to measure the hypertrophy of skeletal muscle fibers. To systematically identify the growth of postnatal…
GSEA error 1005 The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub
I am using the GUI version of GSEA. The samples are of mice. I prepared the required files (.gct) and phenotypelabel (.cls), as required. Expression dataset (partial, feature used are normalized counts) 409 5 NAME description CF355 CF328 WT316 WT351 WT354 ENSMUSG00000025902.14 NA 77 61 110 76 54 ENSMUSG00000102269.2 NA…
Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability
MacDonald SW, Li SC, Bäckman L. Neural underpinnings of within-person variability in cognitive functioning. Psychol Aging. 2009;24:792–808. Article PubMed Google Scholar Haynes BI, Bunce D, Kochan NA, Wen W, Brodaty H, Sachdev PS. Associations between reaction time measures and white matter hyperintensities in very old age. Neuropsychologia. 2017;96:249–55. Article PubMed …
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership | Genome Biology
Models for single-cell ATAC-seq data In single-cell ATAC-seq data, \(x_{ij}\) is the number of unique reads mapping to peak or region j in cell i. Although \(x_{ij}\) can take non-negative integer values, it is common to “binarize” the accessibility data (e.g., [19, 74, 133,134,135]), meaning that \(x_{ij} = 1\) when…
Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin
Mapping eQTLs in patients with psoriasis We obtained longitudinal lesional and non-lesional skin biopsies from participants at baseline, during treatment, and at the time of psoriasis relapse after study medication withdrawal over a course of 22 months. We used genome-wide genotyping and RNA-seq to assay samples. After stringent quality control,…
Bulk RNAseq Standard Data Processing Pipelines
Pipelines and parameters used to process data on the BioBox platform Pipeline for processing public data to sample gene counts SRA-Toolkit is used to fetch the raw files using fasterq-dump -e 3 The files are passed to Kallisto for quantification using kallisto quant -t 3 If the sample is…
C2.CLIN gene sets listing – MSigDB [Broad Insititute]
C2:CLIN:0007 PANCREAS_CHR8_AGUIRRE HG_U133A Human Kate Stafford C2:CLIN:0030 L1_GR_G1 HG_U95Av2 Human Yujin Hoshida C2:CLIN:0006 PANCREAS_CHR7_AGUIRRE HG_U133A Human Kate Stafford C2:CLIN:0029 L0_SM_L1 HG_U95Av2 Human Yujin Hoshida C2:CLIN:0035 G2_SM_G3 HG_U95Av2 Human Yujin Hoshida C2:CLIN:0016 ESC_UP_BHATTACHARYA Gene_Symbol Human Kate Stafford C2:CLIN:0015 IL6_BROCKE HG_U95Av2 Human Kate Stafford C2:CLIN:0014 BCELL_ASTIER HG_U95Av2 Human Kate Stafford C2:CLIN:0031 L1_SM_G1…
Molecular classification of hormone receptor-positive HER2-negative breast cancer
Siegel, R. L., Miller, K. D. & Jemal, A. Cancer statistics, 2020. CA Cancer J. Clin. 70, 7–30 (2020). Article PubMed Google Scholar Huppert, L. A., Gumusay, O., Idossa, D. & Rugo, H. S. Systemic therapy for hormone receptor-positive/human epidermal growth factor receptor 2-negative early stage and metastatic breast cancer….
Which function is best for pathway analysis?
Which function is best for pathway analysis? 1 Hi Biostars, I found there are many function to perform pathway analysis such as fgsea(), gseGO(), gseKEGG(), enrichGO() which made me quite confuse which result I should focus on. Getting a correct background gene set is important. However, how can we find…
Revealing mechanism of Methazolamide for treatment of ankylosing spondylitis based on network pharmacology and GSEA
Braun, J. & Sieper, J. Ankylosing spondylitis. Lancet 369, 1379–1390. doi.org/10.1016/S0140-6736(07)60635-7 (2007). Article PubMed Google Scholar Lai, S. W., Kuo, Y. H. & Liao, K. F. Incidence of inflammatory bowel disease in patients with ankylosing spondylitis. Ann. Rheum. Dis. 80, e144. doi.org/10.1136/annrheumdis-2019-216362 (2021). Article PubMed Google Scholar Bukowski, B. R….
Extending support for mouse data in the Molecular Signatures Database (MSigDB)
The rise of full transcriptome acquisition technologies has fueled the rapid proliferation of molecular-level biological data. These large datasets require interpretation beyond the single-gene level to connect them to meaningful biology and clinical impacts. In 2003, we pioneered the gene set enrichment analysis (GSEA) approach1 to enable the identification of…
Running Enrichr in python using a background gene list
Running Enrichr in python using a background gene list 1 I am trying to run Enrichr in python using a background gene list as per gseapy.readthedocs.io/en/latest/gseapy_example.html (2.3.2.2. Enrichr Web Service (with background input)). I got the following to work without specifying a background: enr_bg = gp.enrichr(gene_list=”3383CCGs.txt”, gene_sets=[‘KEGG_2019_Mouse’], outdir=None ) But…
BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures
Jonsson, A. L. & Bäckhed, F. Role of gut microbiota in atherosclerosis. Nat. Rev. Cardiol. 14, 79–87 (2017). CAS PubMed Google Scholar Tang, W. H. W., Kitai, T. & Hazen, S. L. Gut microbiota in cardiovascular health and disease. Circ. Res. 120, 1183–1196 (2017). CAS PubMed PubMed Central Google Scholar …
Single-cell transcriptomes reveal a molecular link between diabetic kidney and retinal lesions
Animals The animal experiments were approved by the Institutional Animal Care and Use Committee of Jinling Hospital (Nanjing, China), in accordance with the approved guidelines of the Institutional Animal Care and Use Committee of Jinling Hospital. 7 weeks old male wild-type (wt) and leptin receptor-deficient (db/db) mice on the C57BLKS/J…
Bioconductor – GSEABase
DOI: 10.18129/B9.bioc.GSEABase This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GSEABase. Gene set enrichment data structures and methods Bioconductor version: 3.16 This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer:…
Programs To Open .GMT Files
What is a GMT File? A GMT file, also known as Gene Matrix Transposed, is a specific type of file that is extensively used in the field of genomics and bioinformatics. Derived from the title, when a file carries a .gmt extension, it signifies that the file contains a matrix…
Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma
Swerdlow, S. H. et al. The 2016 revision of the World Health Organization classification of lymphoid neoplasms. Blood 127, 2375–2390 (2016). Article CAS PubMed PubMed Central Google Scholar Sehn, L. H. & Salles, G. Diffuse large B-cell lymphoma. N. Engl. J. Med. 384, 842–858 (2021). Article CAS PubMed PubMed Central …
how to check if DE genes are enriched in custom genomic regions derived from epigenetic data
Al , first head to the msigdb website, and take a look at the annotations that belong to set C1: www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C1. Note that, while C1 contains gene sets defined based on position, the others are quite different (e.g. C2 is “curated”, C8 is “cell type signatures”) and so forth. the…
identify cell of origin from bulk RNAseq data
identify cell of origin from bulk RNAseq data 0 Hi, I am trying to figure out what could be the cell of origin (a “nornal” cell type most similar), for a poorly characterized cancer I am workin on, starting from bulk RNAseq data. I have used ssGSEA to generate scores…
Pharmacological targeting of netrin-1 inhibits EMT in cancer
Ye, X. & Weinberg, R. A. Epithelial-mesenchymal plasticity: a central regulator of cancer progression. Trends Cell Biol. 25, 675–686 (2015). Article CAS PubMed PubMed Central Google Scholar Shibue, T. & Weinberg, R. A. EMT, CSCs, and drug resistance: the mechanistic link and clinical implications. Nat. Rev. Clin. Oncol. 14, 611–629…
RARRES2 regulates lipid metabolic reprogramming to mediate the development of brain metastasis in triple negative breast cancer | Military Medical Research
Tumor samples from patients Biopsies of primary breast tumors and breast tumors that had metastasized to the brain were obtained from patients with TNBC at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College. Single-cell RNA sequencing…
Difference between gseapy and gsea
Difference between gseapy and gsea 0 I’m not used to using bioinformatics tools. I’m trying to do a gsea prerank analysis. I used gseapy using python. However, the results seemed different from the gsea analysis used with gsea program from broad institute www.gsea-msigdb.org/gsea/index.jsp the analysis using gseapy from python showed…
GPX4 is a key ferroptosis biomarker and correlated with immune cell populations and immune checkpoints in childhood sepsis
Identification of DE-FRGs in sepsis After the debatch normalization treatment of GSE26378 and GSE26440 (Fig. 2A, Supplementary Figure 1), the differential expression analysis was performed, including 20,021 significantly differentially expressed genes, including 12,758 upregulated genes and 7,263 downregulated genes. log2FC ≥ 1, adjusted P < 0.05 (Fig. 2B). To explore differentially expressed FRG in sepsis, we extracted…
How to Load a Molecular Signature Database into clusterProfiler gseGO?
How to Load a Molecular Signature Database into clusterProfiler gseGO? 0 I am using gseGO this way: gse <- gseGO(geneList=gene_list, ont =”ALL”, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = org.Hs.eg.db, pAdjustMethod = “fdr”) Let’s say I want to analyze against a molecular signature…
Gene Set Comparison Without Expression Data
Gene Set Comparison Without Expression Data 1 I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated with Epidermolysis bullosa shows statistically significant,…
Perform GSEA without gene expression data
Perform GSEA without gene expression data 1 No. GSEA needs expression values to rank gene enrichment between conditions. If you have gene lists, you can look into gene ontology tools which only require gene names or IDs. You can also input your gene list here and select different gene sets…
error related to SnpSift
error related to SnpSift 1 hello everyone, I am trying to use annotate function of snpsift. I have downloaded the software using conda. when i write the command SnpSift this is the output: SnpSift version 4.3t (build 2017-11-24 10:18), by Pablo Cingolani Usage: java -jar SnpSift.jar [command] params… Command is…
Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy
Walhovd, K. B. et al. Neurodevelopmental origins of lifespan changes in brain and cognition. Proc. Natl Acad. Sci. USA 113, 9357–9362 (2016). Article CAS PubMed PubMed Central Google Scholar Damian, R. I., Spengler, M., Sutu, A. & Roberts, B. W. Sixteen going on sixty-six: a longitudinal study of personality stability…
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,…
Integration of bulk RNA sequencing data and single-cell RNA sequencing analysis on the heterogeneity in patients with colorectal cancer
Bao X, Shi R, Zhao T, Wang Y, Anastasov N, Rosemann M et al (2021) Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels tumour heterogeneity plus M2-like tumour-associated macrophage infiltration and aggressiveness in TNBC. Cancer Immunol Immunother 70(1):189–202 Article CAS PubMed Google Scholar Becht E, McInnes L, Healy J,…
Answer: GSEA and GO Ontology
There are a couple of different approaches. 1) you can run similarity and difference metrics on those pathways themselves. for instance, suppose you have three pathways: pathwayA=c(‘A’,’B’,’C’,’D’,’E’,’F’) pathwayB=c(‘A’,’B’,’C’,’D’,’Q’,’F’) pathwayC=c(‘Z’,’Y’,’X’,’W’,’Q’,’J’) pathwayA and B are more similar to each other than pathwayA and pathwayC. You do not need to rely on ontologies…
Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing | BMC Cancer
Single-cell and single-nucleus RNA sequencing of sarcoma subtypes In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing sarcoma (ES), and desmoplastic small round cell tumor (DSRCT) (Fig. 1). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ…
REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2
Standard name REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2 Systematic name M647 Brief description Genes involved in Activated point mutants of FGFR2 Full description or abstract Collection ARCHIVED: Archived Founder gene sets that are referenced by current Hallmarks C2_CP: ARCHIVED Canonical Pathways C2_CP:REACTOME: ARCHIVED Reactome Pathways Source publication Exact source R-HSA-2033519 Related gene sets External…
Genomic and transcriptomic profiling reveal molecular characteristics of parathyroid carcinoma
Clinical and biochemical characteristics of parathyroid carcinoma In total, 50 thyroid tissues were collected from three groups, 12 parathyroid carcinomas, 28 parathyroid adenomas, and 10 normal parathyroid tissues, for genomic and transcriptomic profiling (Fig. 1). The detailed protocols and quality control procedures are described in the Materials and Methods section….
Bioconductor – mastR
DOI: 10.18129/B9.bioc.mastR Markers Automated Screening Tool in R Bioconductor version: Release (3.17) mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from…
Construction of a circRNA-Related ceRNA Prognostic Regulatory Network in Breast Cancer
Introduction Breast cancer is the second most common cancer and is the leading cause of cancer-related death among females worldwide with over 2 million newly diagnosed cases and more than 60 thousand deaths every year.Citation1 Despite advances in treatment, the mortality rate of breast cancer remains high, mainly due to…
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…
Bioinformatics Scientist – TriLab Bioinformatics Core, NIDDK-NIH
Bioinformatician position available at NIH (Bethesda, MD) We seek a bioinformatician/data scientist with a strong record of collaborative interactions with biologists. The successful candidate must have a M.S or Ph.D. degree in bioinformatics, computational biology, computer science, or a related field and have the ability to work independently or as…
RESPIRATORY_CHAIN_COMPLEX_I
Standard name RESPIRATORY_CHAIN_COMPLEX_I Systematic name M13440 Brief description Genes annotated by the GO term GO:0045271. Respiratory chain complex I is an enzyme of the respiratory chain. It consists of at least 34 polypeptide chains and is L-shaped, with a horizontal arm lying in the membrane and a vertical arm that…
STING inhibits the reactivation of dormant metastasis in lung adenocarcinoma
Goddard, E. T., Bozic, I., Riddell, S. R. & Ghajar, C. M. Dormant tumour cells, their niches and the influence of immunity. Nat. Cell Biol. 20, 1240–1249 (2018). Article CAS PubMed Google Scholar Malladi, S. et al. Metastatic latency and immune evasion through autocrine inhibition of WNT. Cell 165, 45–60…
MSigDB SQLite Database – GeneSetEnrichmentAnalysisWiki
From GeneSetEnrichmentAnalysisWiki GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact Introduction With the release of MSigDB 2023.1 we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database…
Bioinformatics analysis of rheumatoid arthritis tissues identifies genes and potential drugs that are expressed specifically
Stephenson, W. et al. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Nat. Commun. 9(1), 791 (2018). Article ADS PubMed PubMed Central Google Scholar Schmidt, C. J. et al. Infection with Clostridioides difficile attenuated collagen-induced arthritis in mice and involved mesenteric Treg and Th2 polarization. Front. Immunol….
msigdbr returns the same genesets for mouse as in for human,
msigdbr returns the same genesets for mouse as in for human, 0 If we were to query the MSigDb database for mouse and human, respectively: mauz <-msigdbr::msigdbr(species=”Mus musculus”) hooman <-msigdbr::msigdbr(species = “Homo sapiens”) And counted the number of genesets from the C8 category, for instance, then both queries would yield…
Battery gene sets for CAMERA limma
Battery gene sets for CAMERA limma 1 @e1fb1374 Last seen 8 hours ago Germany Hi everyone, I’m confused with the results of my CAMERA analysis. For building indexes, I used the battery of gene sets from MSigDb. I transformed the gmt files to list and built indexes. The initial count…
MITOCHONDRIAL_RESPIRATORY_CHAIN
Standard name MITOCHONDRIAL_RESPIRATORY_CHAIN Systematic name M19046 Brief description Genes annotated by the GO term GO:0005746. The protein complexes that form the mitochondrial electron transport system (the respiratory chain). Complexes I, III and IV can transport protons if embedded in an oriented membrane, such as an intact mitochondrial inner membrane. Full…
Rare coding variants as risk modifiers of the 22q11.2 deletion implicate postnatal cortical development in syndromic schizophrenia
Edelmann L, Pandita RK, Morrow BE. Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. Am J Hum Genet. 1999;64:1076–86. Article CAS PubMed PubMed Central Google Scholar Shaikh TH, Kurahashi H, Saitta SC, O’Hare AM, Hu P, Roe BA, et al. Chromosome 22-specific low copy repeats and…
Combined scRNAseq and Bulk RNAseq Analysis to Reveal the Dual Roles of Oxidative Stress-Related Genes in Acute Myeloid Leukemia
Background. Oxidative stress (OS) can either lead to leukemogenesis or induce tumor cell death by inflammation and immune response accompanying the process of OS through chemotherapy. However, previous studies mainly focus on the level of OS state and the salient factors leading to tumorigenesis and progression of acute myeloid leukemia…
Maternal diet induces persistent DNA methylation changes in the muscle of beef calves
Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS Google Scholar Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS Google Scholar Encinias, H. B., Lardy,…
GSEA on nonmodel organisms
GSEA on nonmodel organisms 2 Hi, I want to do GSEA analysis in R on significantly differentially expressed genes on nonmodel species (five in total). My research is based on cross-species comparative transcriptomics. And this is what I am doing: I already have species-specific: de novo assemblies, annotations (across 7…
Predicting severity in COVID-19 disease using sepsis blood gene expression signatures
Mechanisms of sepsis severity and mortality in COVID-19 patients To identify COVID-19 specific severity mechanisms, we initially compared the whole blood gene expression profiles associated with defined severity groups from a cohort of 124 patients recruited at various times relative to hospital admission. Patient severity was assessed using two measures,…
Population-level variation in enhancer expression identifies disease mechanisms in the human brain
Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central Article CAS Google Scholar Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central …
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data
Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central Article Google Scholar Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….
Subtype and cell type specific expression of lncRNAs provide insight into breast cancer
lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer
Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…
Gene Set – TNFSF10
Dataset MSigDB Cancer Gene Co-expression Modules Category transcriptomics Type co-expressed gene Description tumor necrosis factor (ligand) superfamily, member 10|The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not…
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…
Two drugs show promise in rejuvenating lung epithelial progenitor cells damaged by COPD
Overview of the transcriptomics-guided drug discovery strategy.(A) Schematic outline of the drug screening strategy. (B) Heatmap shows the gene expression pattern of the druggable genes (www.dgidb.org) identified both in CS-exposed mice and patient with COPD databases. (C) Reactome pathway enrichment analysis of genes differentially expressed from patients with COPD (8)…
Immune-related Prognostic Genes of ccRCC
Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics
1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article Google Scholar 2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…
Hypoxic Characteristic Genes Predict Response to Immunotherapy for Urothelial Carcinoma
This article was originally published here Front Cell Dev Biol. 2021 Nov 25;9:762478. doi: 10.3389/fcell.2021.762478. eCollection 2021. ABSTRACT Objective: Resistance to immune checkpoint inhibitors (ICIs) has been a massive obstacle to ICI treatment in metastatic urothelial carcinoma (MUC). Recently, increasing evidence indicates the clinical importance of the association between hypoxia…
KINNEY_DNMT1_METHYLATION_TARGETS
Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…
Identification of lipid metabolism-associated gene signature
Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…
Classifiers for predicting coronary artery disease
Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…
Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis (GSEA)
Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis (GSEA) 1 Hi all, I am new to bioinformatics and am currently learning how to use GSEA. Background: I analyzed my RNA-Seq results using DESeq2, and am now learning to perform GSEA. For my project, in broad terms, I…
Gene expression profiling of contralateral dorsal root gangl
Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…
Error in loading files into the GSEA software
Error in loading files into the GSEA software 0 Hi everyone I have some trouble with my RNA-seq file when I try to upload it for analysis with GSEA. I am getting the following error: Can anyone help me fix it? many thanks! —- Full Error Message —- There were…
Bioconductor – SingscoreAMLMutations
DOI: 10.18129/B9.bioc.SingscoreAMLMutations Using singscore to predict mutations in AML from transcriptomic signatures Bioconductor version: Release (3.13) This workflow package shows how transcriptomic signatures can be used to infer phenotypes. The workflow begins by showing how the TCGA AML transcriptomic data can be downloaded and processed using the TCGAbiolinks…
working with .gmt files
working with .gmt files 3 Hi! I have downloaded a pathway data set in .gmt format form the GSEA website. I’m wondering how can I properly read this data set in R. Could anyone help me? Thank you! myposts • 9.5k views • link updated 2 hours ago by…
Performing GSEA using MSigDB gene sets in R
Performing GSEA using MSigDB gene sets in R 2 I am trying to perform a gene set enrichment analysis in r using the gene sets available from msigdb and a list of gene names from my own data set. I am able to to use the msigdbr library to import…