scholarly journals lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs

2019 ◽  
Author(s):  
Fayaz Seifuddin ◽  
Komudi Singh ◽  
Abhilash Suresh ◽  
Yun-Ching Chen ◽  
Vijender Chaitankar ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Gene Expression Profiles ◽  
Tissue Expression ◽  
Whole Genome Sequencing Data ◽  
Specific Gene ◽  
Solid Organ ◽  
Sequencing Data ◽  
Additional Information ◽  
Gene Modules

ABSTRACTWe have assembled a comprehensivelongnon-codingRNAknowledgebase (lncRNAKB) of 77,199 annotated human lncRNAs (224,286 transcripts) by methodically integrating widely used lncRNAs resources. To facilitate functional characterization of lncRNAs, we employed Genotype-Tissue Expression (GTEx) project to provide tissue-specific gene expression profiles of lncRNAs in 31 solid organ tissues. Additional information includes network analysis to identify co-expressed gene modules to potentially delineate lncRNA function. Tissue-specificity, phylogenetic conservation scores and coding potential for lncRNAs are included. Finally, using whole genome sequencing data from GTEx, expression quantitative trait loci (cis-eQTL) regulated lncRNAs were calculated in all tissues. lncRNAKB is available athttp://www.lncrnakb.org.

scholarly journals Diurnal.plant.tools: comparative transcriptomic and co-expression analyses of diurnal gene expression of the Archaeplastida kingdom

2019 ◽  
Author(s):  
Jonathan Wei Xiong Ng ◽  
Qiao Wen Tan ◽  
Camilla Ferrari ◽  
Marek Mutwil
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Species Comparisons ◽  
Gene Modules ◽  
Time Specific ◽  
Almost All ◽  
User Friendly ◽  
Diurnal Regulation

ABSTRACTAlmost all organisms coordinate some aspects of their biology through the diurnal cycle. Photosynthetic organisms, and plants especially, have established complex programs that coordinate physiological, metabolic and developmental processes with the changing light. The diurnal regulation of the underlying transcriptional processes is observed when groups of functionally related genes (gene modules) are expressed at a specific time of the day. However, studying the diurnal regulation of these gene modules in the plant kingdom was hampered by the large amount of data required for the analyses. To meet this need, we used gene expression data from 17 diurnal studies spanning the whole Archaeplastida kingdom (Plantae kingdom in the broad sense) to make an online diurnal database. We have equipped the database with tools that allow user-friendly cross-species comparisons of gene expression profiles, entire co-expression networks, co-expressed clusters (involved in specific biological processes), time-specific gene expression, and others. We exemplify how these tools can be used by studying three important biological questions: (i) the evolution of cell division, (ii) the diurnal control of gene modules in algae and (iii) the conservation of diurnally-controlled modules across species. The database is freely available at http://diurnal.plant.tools/.

scholarly journals Diurnal.plant.tools: Comparative Transcriptomic and Co-expression Analyses of Diurnal Gene Expression of the Archaeplastida Kingdom

2019 ◽  
Vol 61 (1) ◽  
pp. 212-220 ◽  
Author(s):  
Jonathan Wei Xiong Ng ◽  
Qiao Wen Tan ◽  
Camilla Ferrari ◽  
Marek Mutwil
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Species Comparisons ◽  
Gene Modules ◽  
Time Specific ◽  
Almost All ◽  
User Friendly ◽  
Diurnal Regulation

Abstract Almost all organisms coordinate some aspects of their biology through the diurnal cycle. Photosynthetic organisms, and plants especially, have established complex programs that coordinate physiological, metabolic and developmental processes with the changing light. The diurnal regulation of the underlying transcriptional processes is observed when groups of functionally related genes (gene modules) are expressed at a specific time of the day. However, studying the diurnal regulation of these gene modules in the plant kingdom was hampered by the large amount of data required for the analyses. To meet this need, we used gene expression data from 17 diurnal studies spanning the whole Archaeplastida kingdom (Plantae kingdom in the broad sense) to make an online diurnal database. We have equipped the database with tools that allow user-friendly cross-species comparisons of gene expression profiles, entire co-expression networks, co-expressed clusters (involved in specific biological processes), time-specific gene expression and others. We exemplify how these tools can be used by studying three important biological questions: (i) the evolution of cell division, (ii) the diurnal control of gene modules in algae and (iii) the conservation of diurnally controlled modules across species. The database is freely available at http://diurnal.plant.tools.

scholarly journals Transcriptomic and Single-Cell Analysis of the Murine Parotid Gland

2019 ◽  
Vol 98 (13) ◽  
pp. 1539-1547 ◽  
Author(s):  
A. Oyelakin ◽  
E.A.C. Song ◽  
S. Min ◽  
J.E. Bard ◽  
J.V. Kann ◽  
...  
Keyword(s):  
Parotid Gland ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Cell Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Biological Properties ◽  
Cellular Heterogeneity ◽  
Specific Gene ◽  
Sequencing Data

The salivary complex of mammals consists of 3 major pairs of glands: the parotid, submandibular, and sublingual glands. While the 3 glands share similar functional properties, such as saliva secretion, their differences are largely based on the types of secretions they produce. While recent studies have begun to shed light on the underlying molecular differences among the glands, few have examined the global transcriptional repertoire over various stages of gland maturation. To better elucidate the molecular nature of the parotid gland, we have performed RNA sequencing to generate comprehensive and global gene expression profiles of this gland at different stages of maturation. Our transcriptomic characterization and hierarchical clustering analysis with adult organ RNA sequencing data sets has identified a number of molecular players and pathways that are relevant for parotid gland biology. Moreover, our detailed analysis has revealed a unique parotid gland–specific gene signature that may represent important players that could impart parotid gland–specific biological properties. To complement our transcriptomic studies, we have performed single-cell RNA sequencing to map the transcriptomes of parotid epithelial cells. Interrogation of the single-cell transcriptomes revealed the degree of molecular and cellular heterogeneity of the various epithelial cell types within the parotid gland. Moreover, we uncovered a mixed-lineage population of cells that may reflect molecular priming of differentiation potentials. Overall our comprehensive studies provide a powerful tool for the discovery of novel molecular players important in parotid gland biology.

scholarly journals Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders

2021 ◽  
Vol 15 ◽  
Author(s):  
Junlin Shen ◽  
Bingbing Yang ◽  
Zhonghua Xie ◽  
Heng Wu ◽  
Zhanye Zheng ◽  
...  
Keyword(s):  
Brain Activity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Brain Disorders ◽  
Cell Type ◽  
Spontaneous Brain Activity ◽  
Cell Type Specific ◽  
Gene Modules ◽  
Molecular Substrates

Mapping gene expression profiles to neuroimaging phenotypes in the same anatomical space provides opportunities to discover molecular substrates for human brain functional properties. Here, we aimed to identify cell-type-specific gene modules associated with the regional homogeneity (ReHo) of spontaneous brain activity and their associations with brain disorders. Fourteen gene modules were consistently associated with ReHo in the three datasets, five of which showed cell-type-specific expression (one neuron-endothelial module, one neuron module, one astrocyte module and two microglial modules) in two independent cell series of the human cerebral cortex. The neuron-endothelial module was mainly enriched for transporter complexes, the neuron module for the synaptic membrane, the astrocyte module for amino acid metabolism, and microglial modules for leukocyte activation and ribose phosphate biosynthesis. In enrichment analyses of cell-type-specific modules for 10 common brain disorders, only the microglial module was significantly enriched for genes obtained from genome-wide association studies of multiple sclerosis (MS) and Alzheimer’s disease (AD). The ReHo of spontaneous brain activity is associated with the gene expression profiles of neurons, astrocytes, microglia and endothelial cells. The microglia-related genes associated with MS and AD may provide possible molecular substrates for ReHo abnormality in both brain disorders.

scholarly journals LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Ren ◽  
Ting-You Wang ◽  
Leah C. Anderton ◽  
Qi Cao ◽  
Rendong Yang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Clinical Samples ◽  
Sequencing Data ◽  
Multiple Cancer ◽  
Regulatory Pathways ◽  
Cancer Transcriptome ◽  
Versatile Tool

Abstract Background Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRNAs followed by gene expression profiling in cancer cell lines are established approaches to address this problem, these experimental data are not available for a majority of the annotated lncRNAs. Results As a surrogate, we present lncGSEA, a convenient tool to predict the lncRNA associated pathways through Gene Set Enrichment Analysis of gene expression profiles from large-scale cancer patient samples. We demonstrate that lncGSEA is able to recapitulate lncRNA associated pathways supported by literature and experimental validations in multiple cancer types. Conclusions LncGSEA allows researchers to infer lncRNA regulatory pathways directly from clinical samples in oncology. LncGSEA is written in R, and is freely accessible at https://github.com/ylab-hi/lncGSEA.

Genome-wide systematic characterization and its regulatory expression reprogramming process of the bZIP transcription factors during trauma response in Camellia sinensis

2018 ◽  
Vol 48 (11) ◽  
pp. 1279-1291
Author(s):  
Yajie Xue ◽  
Zaibao Zhang ◽  
Lei Wang ◽  
Yajun Yu ◽  
Jinbin Xiao ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Camellia Sinensis ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Gene Expression Profiles ◽  
Bzip Transcription Factor ◽  
Motif Analysis ◽  
Basic Leucine Zipper ◽  
Tea Tree

Basic leucine zipper (bZIP) transcription factor (TF) genes regulate numerous biological processes, as well as biotic and abiotic responses. Although the genome of the tea tree (Camellia sinensis (L.) Kuntze) has been released, knowledge regarding the bZIP TF family in C. sinensis, e.g., phylogenetic relationship and transcriptional gene expression profiles, remains limited. In this study, we characterized 77 bZIP genes in C. sinensis based on transcriptomic and genomic data and divided them into 11 groups according to their phylogenetic relationship with those in Arabidopsis, which allowed us to identify 14 pairs of orthologous proteins shared by Arabidopsis and C. sinensis and 19 pairs of paralogous proteins in C. sinensis. Conserved motif analysis of CsbZIP proteins showed high group specificity. Our classification was supported by the predicted specificities based on DNA-binding domains, as well as the dimerization property based on characteristic features in the basic and hinge regions and the leucine zipper. Specifically, they indicated that some highly conserved amino acid residues exist across each major group in the tree of land plant life. Expression profiling analyses indicate that the CsbZIP genes are likely involved in response to trauma, and a model was established to display the unique expression of each group during different time intervals after wounding. This work provides useful clues for further functional characterization of the CsbZIP TFs.

scholarly journals Convergent evolution of venom gland transcriptomes across Metazoa

2021 ◽  
Author(s):  
Giulia Zancolli ◽  
Maarten Reijnders ◽  
Robert Waterhouse ◽  
Marc Robinson-Rechavi
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Venom Gland ◽  
Bioactive Molecules ◽  
Specific Gene ◽  
Animal Kingdom ◽  
Venom Glands

Animals have repeatedly evolved specialized organs and anatomical structures to produce and deliver a cocktail of potent bioactive molecules to subdue prey or predators: venom. This makes it one of the most widespread convergent functions in the animal kingdom. Whether animals have adopted the same genetic toolkit to evolved venom systems is a fascinating question that still eludes us. Here, we performed the first comparative analysis of venom gland transcriptomes from 20 venomous species spanning the main Metazoan lineages, to test whether different animals have independently adopted similar molecular mechanisms to perform the same function. We found a strong convergence in gene expression profiles, with venom glands being more similar to each other than to any other tissue from the same species, and their differences closely mirroring the species phylogeny. Although venom glands secrete some of the fastest evolving molecules (toxins), their gene expression does not evolve faster than evolutionarily older tissues. We found 15 venom gland specific gene modules enriched in endoplasmic reticulum stress and unfolded protein response pathways, indicating that animals have independently adopted stress response mechanisms to cope with mass production of toxins. This, in turns, activates regulatory networks for epithelial development, cell turnover and maintenance which seem composed of both convergent and lineage-specific factors, possibly reflecting the different developmental origins of venom glands. This study represents the first step towards an understanding of the molecular mechanisms underlying the repeated evolution of one of the most successful adaptive traits in the animal kingdom.

Dimethyl fumarate induces ferroptosis and impairs NF-κB/STAT3 signaling in DLBCL

Blood ◽  
2021 ◽  
Author(s):  
Anja Schmitt ◽  
Wendan Xu ◽  
Philip Bucher ◽  
Melanie Grimm ◽  
Martina Konantz ◽  
...  
Keyword(s):  
Cell Death ◽  
B Cell ◽  
Expression Profiles ◽  
Therapeutic Option ◽  
Gene Expression Profiles ◽  
B Cell Lymphoma ◽  
Dimethyl Fumarate ◽  
Specific Gene ◽  
Molecular Heterogeneity ◽  
Stat3 Signaling

Despite the development of novel targeted drugs, the molecular heterogeneity of diffuse large B-cell lymphoma (DLBCL) still poses a major therapeutic challenge. DLBCL can be classified into at least two major subtypes, i.e. germinal center B-cell-like (GCB) and the aggressive activated B-cell-like (ABC) DLBCL, each characterized by specific gene expression profiles and mutation patterns. Here we demonstrate a broad anti-tumor effect of dimethyl fumarate (DMF) on both DLBCL subtypes, which is mediated by the induction of ferroptosis, a form of cell death driven by the peroxidation of phospholipids. Due to high expression of arachidonate 5-lipoxygenase in concert with low glutathione and glutathione peroxidase 4 levels, DMF induces lipid peroxidation and thus ferroptosis particularly in GCB DLBCL. In ABC DLBCL cells, which are addicted to NF-κB and STAT3 survival signaling, DMF treatment efficiently inhibits the activity of the IKK complex and JAK kinases. Interestingly, the BCL-2 specific BH3 mimetic ABT-199 and an inhibitor of ferroptosis suppressor protein 1 synergize with DMF in inducing cell death in DLBCL. Collectively, our findings identify the clinically approved drug DMF as a promising novel therapeutic option in the treatment of both GCB and ABC DLBCL.

scholarly journals Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Fredrik Barrenas ◽  
Kevin Raehtz ◽  
Cuiling Xu ◽  
Lynn Law ◽  
Richard R. Green ◽  
...  
Keyword(s):  
Wound Healing ◽  
Expression Profiles ◽  
Healing Process ◽  
Gene Expression Profiles ◽  
Gene Signature ◽  
African Green Monkey ◽  
Wound Healing Process ◽  
Sequencing Data ◽  
Green Monkey ◽  
Conserved Gene

Abstract Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-β and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.

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