Abstract：
:Transcription control plays a crucial role in establishing a unique gene expression signature for each of the hundreds of mammalian cell types. Though gene expression data have been widely used to infer cellular regulatory networks, existing methods mainly infer correlations rather than causality. We developed statistical models and likelihood-ratio tests to infer causal gene regulatory networks using enhancer RNA (eRNA) expression information as a causal anchor and applied the framework to eRNA and transcript expression data from the FANTOM Consortium. Predicted causal targets of transcription factors (TFs) in mouse embryonic stem cells, macrophages and erythroblastic leukaemia overlapped significantly with experimentally-validated targets from ChIP-seq and perturbation data. We further improved the model by taking into account that some TFs might act in a quantitative, dosage-dependent manner, whereas others might act predominantly in a binary on/off fashion. We predicted TF targets from concerted variation of eRNA and TF and target promoter expression levels within a single cell type, as well as across multiple cell types. Importantly, TFs with high-confidence predictions were largely different between these two analyses, demonstrating that variability within a cell type is highly relevant for target prediction of cell type-specific factors. Finally, we generated a compendium of high-confidence TF targets across diverse human cell and tissue types.
journal_name
Int J Mol Scijournal_title
International journal of molecular sciencesauthors
Vipin D,Wang L,Devailly G,Michoel T,Joshi Adoi
10.3390/ijms19113609subject
Has Abstractpub_date
2018-11-15 00:00:00issue
11issn
1422-0067pii
ijms19113609journal_volume
19pub_type
杂志文章abstract：:Aging is an inevitable and gradually progressive process affecting all organs and systems. The musculoskeletal system makes no exception, elderly exhibit an increased risk of sarcopenia (low muscle mass),dynapenia (declining muscle strength), and subsequent disability. Whereas in recent years the subject of skeletal m...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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更新日期：2020-01-16 00:00:00
abstract：:Spondyloarthritis (SpA) is a subset of seronegative rheumatic-related autoimmune diseases that consist of ankylosing spondylitis (AS), psoriatic spondylitis (PsA), reactive spondylitis (re-SpA), inflammatory bowel disease (IBD)-associated spondylitis, and unclassifiable spondylitis. These subsets share clinical phenot...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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更新日期：2020-09-03 00:00:00
abstract：:Apocynin, also known as acetovanillone, is a natural organic compound structurally related to vanillin. Apocynin is known to be an inhibitor of NADPH (Nicotinamide adenine dinucleotide phosphate) oxidase activity and is highly effective in suppressing the production of superoxide. The neuroprotective effects of apocyn...
journal_title：International journal of molecular sciences
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更新日期：2018-10-09 00:00:00
abstract：:Aging is a major risk factor of osteoarthritis, which is characterized by the degeneration of articular cartilage. CCN3, a member of the CCN family, is expressed in cartilage and has various physiological functions during chondrocyte development, differentiation, and regeneration. Here, we examine the role of CCN3 in ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21207556
更新日期：2020-10-13 00:00:00
abstract：:Esophageal squamous cell carcinoma (ESCC), a major histologic type of esophageal cancer, is one of the frequent causes of cancer-related death worldwide. Picropodophyllotoxin (PPT) is the main component of Podophyllum hexandrum root with antitumor activity via apoptosis-mediated mechanisms in several cancer cells. How...
journal_title：International journal of molecular sciences
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更新日期：2020-06-30 00:00:00
abstract：:Unlike orthodox species, seed recalcitrance is poorly understood, especially at the molecular level. In this regard, seed maturation and germination were studied in the non-orthodox Quercus ilex by using a proteomics strategy based on two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ioni...
journal_title：International journal of molecular sciences
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更新日期：2020-07-09 00:00:00
abstract：:Primary biliary cholangitis (PBC) is an immune-mediated cholestatic disease. Vitamin D receptor (VDR)-dependent signaling constrains an inflammatory response by targeting the miRNA155-SOCS1 (suppressor of cytokine signaling 1) axis. The VDR-miRNA155-SOCS1 pathway was investigated in the context of the autoimmune respo...
journal_title：International journal of molecular sciences
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更新日期：2017-01-29 00:00:00
abstract：:Cancer vaccines may be harnessed to incite immunity against poorly immunogenic tumors, however they have failed in therapeutic settings. Poor antigenicity coupled with systemic and intratumoral immune suppression have been significant drawbacks. RNA encoding for tumor associated or specific epitopes can serve as a mor...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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更新日期：2018-09-23 00:00:00
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journal_title：International journal of molecular sciences
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更新日期：2020-03-10 00:00:00
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journal_title：International journal of molecular sciences
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doi：10.3390/ijms13078219
更新日期：2012-01-01 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
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更新日期：2020-02-16 00:00:00
abstract：:Endoplasmic reticulum stress (ERS) is one of the mechanisms of apoptotic cell death. Inhibiting the apoptosis induced by ERS may be a novel therapeutic target in cardiovascular diseases. Icariin, a flavonoid isolated from Epimedium brevicornum Maxim, has been demonstrated to have cardiovascular protective effects, but...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms140917845
更新日期：2013-08-30 00:00:00
abstract：:We characterized Schistosoma japonicum HSP40 (Sjp40) and HSP90α (Sjp90α) in this study. Western blot analysis revealed both are present in soluble egg antigens and egg secretory proteins, implicating them in triggering the host immune response after secretion from eggs into host tissues. These observations were confir...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21114034
更新日期：2020-06-04 00:00:00
abstract：:Epithelial-mesenchymal transition (EMT) is a key process in cancer development and progression. Communication (crosstalk) between cancer cells and normal (nonmalignant) cells may facilitate cancer progression. Conditioned medium (CM) obtained from cultured cancer cells contains secreted factors capable of affecting ph...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms18081528
更新日期：2017-08-01 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms150814396
更新日期：2014-08-18 00:00:00
abstract：:The enzyme Cypridina luciferase (CLase) enables Cypridina luciferin to emit light efficiently through an oxidation reaction. The catalytic mechanism on the substrate of CLase has been studied, but the details remain to be clarified. Here, we examined the luminescence of Cypridina luciferin in the presence of several p...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21207516
更新日期：2020-10-12 00:00:00
abstract：:The abundance of intrinsic disorder in the protein realm and its role in a variety of physiological and pathological cellular events have strengthened the interest of the scientific community in understanding the structural and dynamical properties of intrinsically disordered proteins (IDPs) and regions (IDRs). Attemp...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms21176208
更新日期：2020-08-27 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms19010012
更新日期：2017-12-21 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms20010121
更新日期：2018-12-29 00:00:00
abstract：:The rapidly activating delayed rectifier potassium current (IKr) plays a critical role in cardiac repolarization. Although IKr is known to be regulated by both α1- and β1-adrenergic receptors (ARs), the cross-talk and feedback mechanisms that dictate its response to α1- and β1-AR activation are not known. In the prese...
journal_title：International journal of molecular sciences
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journal_title：International journal of molecular sciences
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更新日期：2020-05-18 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms20246235
更新日期：2019-12-10 00:00:00
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journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms9101977
更新日期：2008-10-01 00:00:00
abstract：:Regorafenib eye drops were developed for treating age-related macular degeneration. This study aimed to investigate the effects of this multi-kinase inhibitor on intraocular pressure (IOP), bleb formation, and conjunctival changes in a canine filtration surgery model. Glaucoma filtration surgery models were created in...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21010063
更新日期：2019-12-20 00:00:00
abstract：:Recent studies have demonstrated that exosomal microRNAs (miRNAs) have the potential of facilitating molecular diagnosis. Currently, little is known about the underlying mechanism behind late-onset acute graft-versus-host disease (LA GVHD). Identifying differentially expressed miRNAs in exosomes should be useful for u...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms19092493
更新日期：2018-08-23 00:00:00
abstract：:The bone-derived hormone fibroblast growth factor 23 (FGF23) acts in concert with parathyroid hormone (PTH) and the active vitamin D metabolite calcitriol in the regulation of calcium (Ca) and phosphate (P) homeostasis. More factors are being identified to regulate FGF23 levels and the endocrine loops between the thre...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms21228810
更新日期：2020-11-20 00:00:00
abstract：:The terpolymerization of carbon dioxide (CO₂), propylene oxide (PO), and cyclohexene oxide (CHO) were performed by both random polymerization and block polymerization to synthesize the random poly (propylene cyclohexene carbonate) (PPCHC), di-block polymers of poly (propylene carbonate⁻cyclohexyl carbonate) (PPC-PCHC)...
journal_title：International journal of molecular sciences
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更新日期：2018-11-23 00:00:00
abstract：:Chimeric antigen receptors (CARs) have found clinical success in B cell malignancies, but a dearth of potential targets limits their wider clinical application, especially in solid tumours. Here, we describe the development of an anti-annexin A2 CAR, CAR(2448), derived from an antibody found to have activity against e...
journal_title：International journal of molecular sciences
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doi：10.3390/ijms21020381
更新日期：2020-01-07 00:00:00
abstract：:In this study, we optimized the geometry and composition of additive-manufactured pedicle screws. Metal powders of titanium-aluminum-vanadium (Ti-6Al-4V) were mixed with reactive glass-ceramic biomaterials of bioactive glass (BG) powders. To optimize the geometry of pedicle screws, we applied a novel numerical approac...
journal_title：International journal of molecular sciences
pub_type： 杂志文章
doi：10.3390/ijms21207438
更新日期：2020-10-09 00:00:00
abstract：:The endoplasmic reticulum (ER) is the principal organelle responsible for correct protein folding, a step in protein synthesis that is critical for the functional conformation of proteins. ER stress is a primary feature of secretory cells and is involved in the pathogenesis of numerous human diseases, such as certain ...
journal_title：International journal of molecular sciences
pub_type： 杂志文章,评审
doi：10.3390/ijms17020192
更新日期：2016-02-01 00:00:00
