Integrative analyses of genes associated with idiopathic pulmonary fibrosis.


:Idiopathic pulmonary fibrosis (IPF), characterized by irreversible scarring and progressive destruction of the lung tissue, is one of the most common types of idiopathic interstitial pneumonia worldwide. However, there are no reliable candidates for curative therapies. Hence, elucidation of the mechanisms of IPF genesis and exploration of potential biomarkers and prognostic indicators are essential for accurate diagnosis and treatment of IPF. Recently, efficient microarray and bioinformatics analyses have promoted an understanding of the molecular mechanisms of disease occurrence and development, which is necessary to explore genetic alternations and identify potential diagnostic biomarkers. However, high false-positive rates results have been observed based on single microarray datasets. In the current study, we performed a comprehensive analysis of the differential expression, biological functions, and interactions of IPF-related genes. Three publicly available microarray datasets including 54 IPF samples and 34 normal samples were integrated by performing gene set enrichment analysis and analyzing differentially expressed genes (DEGs). Our results identified 350 DEGs genetically associated with IPF. Gene ontology analyses revealed that the changes in the modules were mostly enriched in the positive regulation of smooth muscle cell proliferation, positive regulation of inflammatory responses, and the extracellular space. Kyoto encyclopedia of genes and genomes enrichment analysis of DEGs revealed that IPF involves the TNF signaling pathway, NOD-like receptor signaling pathway, and PPAR signaling pathway. To identify key genes related to IPF in the protein-protein interaction network, 20 hub genes were screened out with highest scores. Our results provided a framework for developing new pathological molecular networks related to specific diseases in silico.


J Cell Biochem


Wang H,Xie Q,Ou-Yang W,Zhang M




Has Abstract


2018-12-02 00:00:00






  • Ebselen inhibits the activity of acetylcholinesterase globular isoform G4 in vitro and attenuates scopolamine-induced amnesia in mice.

    abstract::There is a well-known relationship between the cholinergic system and learning, memory, and other common cognitive processes. The process for researching and developing new drugs has lead researchers to repurpose older ones. This study investigated the effects of ebselen on the activity of acethylcholinesterase (AChE)...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Martini F,Pesarico AP,Brüning CA,Zeni G,Nogueira CW

    更新日期:2018-07-01 00:00:00

  • Notch-1 inhibits apoptosis in murine erythroleukemia cells and is necessary for differentiation induced by hybrid polar compounds.

    abstract::Strikingly increased expression of notch-1 has been demonstrated in several human malignancies and pre-neoplastic lesions. However, the functional consequences of notch-1 overexpression in transformed cells remain unclear. We investigated whether endogenously expressed notch-1 controls cell fate determination in mouse...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Shelly LL,Fuchs C,Miele L

    更新日期:1999-05-01 00:00:00

  • Imaging UVC-induced DNA damage response in models of minimal cancer.

    abstract::We have previously demonstrated that the ultraviolet (UV) light is effective against a variety of cancer cells in vivo as well as in vitro. In the present report, we imaged the DNA damage repair response of minimal cancer after UVC irradiation. DNA-damage repair response to UV irradiation was imaged on tumors growing ...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Miwa S,Yano S,Hiroshima Y,Tome Y,Uehara F,Mii S,Efimova EV,Kimura H,Hayashi K,Tsuchiya H,Hoffman RM

    更新日期:2013-11-01 00:00:00

  • Gamma-secretase inhibitor suppressed Notch1 intracellular domain combination with p65 and resulted in the inhibition of the NF-κB signaling pathway induced by IL-1β and TNF-α in nucleus pulposus cells.

    abstract::In this experiment, the cross-talk betweenNotch and the NF-κB signaling pathway was examined to reveal the mechanism of slowing down the type II collagen (ColII) and aggrecan degeneration affected by inflammatory cytokines. The expression levels of ColII and aggrecan in the intervertebral disc were observed through im...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Huang Y,Mei W,Chen J,Jiang T,Zhou Z,Yin G,Fan J

    更新日期:2018-10-26 00:00:00

  • Differential display of human marrow stromal cells reveals unique mRNA expression patterns in response to dexamethasone.

    abstract::Human bone marrow stromal cells (hBMSC) are pluripotent cells that have the ability to differentiate into bone, cartilage, hematopoietic-supportive stroma, and adipocytes in a process modulated by dexamethasone (DEX). To characterize changes in hBMSC in response to DEX, we carried out differential display experiments ...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Dieudonné SC,Kerr JM,Xu T,Sommer B,DeRubeis AR,Kuznetsov SA,Kim IS,Gehron Robey P,Young MF

    更新日期:1999-12-01 00:00:00

  • Giant cell tumor of bone: a unique paradigm of stromal-hematopoietic cellular interactions.

    abstract::Giant cell tumor of bone is a progressive, potentially malignant process which destroys skeletal tissue by virtue of its osteoclast complement. As a biological entity it provides a unique natural model of bone resorption by osteoclasts whose recruitment and development is controlled by a neoplastic population of fibro...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章,评审


    authors: Robinson D,Einhorn TA

    更新日期:1994-07-01 00:00:00

  • Interaction of the low-molecular-weight GTP-binding protein rap2 with the platelet cytoskeleton is mediated by direct binding to the actin filaments.

    abstract::The interaction of the low-molecular-weight GTP-binding protein rap2 with the cytoskeleton from thrombin-aggregated platelets was investigated by inducing depolymerization of the actin filaments, followed by in vitro-promoted repolymerization. We found that the association of rap2 with the cytoskeleton was spontaneous...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Torti M,Bertoni A,Canobbio I,Sinigaglia F,Lapetina EG,Balduini C

    更新日期:1999-12-15 00:00:00

  • A synthetic fragment of leptin increase hematopoietic stem cell population and improve its engraftment ability.

    abstract::Several studies have shown the important actions of cytokine leptin that regulates food intake and energy expenditure. Additionally, the ability to modulate hematopoiesis has also been demonstrated. Previous reports have shown that some synthetic sequences of leptin molecules can activate leptin receptor. Herein, deca...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Dias CC,Nogueira-Pedro A,Tokuyama PY,Martins MN,Segreto HR,Buri MV,Miranda A,Paredes-Gamero EJ

    更新日期:2015-07-01 00:00:00

  • Sex-specific effects of estrogen and androgen on gene expression in human monocyte-derived osteoclasts.

    abstract::Estrogen and androgen are both critical for the maintenance of bone, but the target cells, mechanisms, and responses could be sex-specific. To compare sex-specific actions of estrogen and androgen on osteoclasts, human peripheral blood mononuclear precursor cells from adult Caucasian males (n = 3) and females (n = 3) ...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Wang J,Stern PH

    更新日期:2011-12-01 00:00:00

  • Characterization of tumors produced by signal peptide-basic fibroblast growth factor-transformed cells.

    abstract::Basic fibroblast growth factor (bFGF) is found in a variety of cells and tissues. We have previously shown that bFGF is a transforming growth factor, but only when fused to a signal peptide (sp-bFGF). Cells expressing the native bFGF are tumorigenic in nude mice only, where the tumors form at a low frequency and grow ...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Rogelj S,Weinberg RA,Fanning P,Klagsbrun M

    更新日期:1989-01-01 00:00:00

  • High-level expression of endogenous acid phosphatase inhibits growth and vectorial secretion in Saccharomyces cerevisiae.

    abstract::The secretion pathway of Saccharomyces cerevisiae was challenged by constitutively overexpressing plasmid-encoded acid phosphatase, a secreted endogenous glycoprotein. A 2-microns-based multicopy plasmid carrying the coding sequence of acid phosphatase under the control of a truncated variant of the strong constitutiv...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Kleene R,Janes M,Meyhack B,Pulfer K,Hinnen A

    更新日期:1995-02-01 00:00:00

  • The mammalian iris-ciliary complex affects organization and synthesis of cytoskeletal proteins of organ and tissue cultured lens epithelial cells.

    abstract::A water soluble growth inhibitor was isolated from the mammalian ocular iris-ciliary complex. The molecular weight of this protein is 10 kD or lower as determined by ultrafiltration fractionation. The iris-ciliary (IC) complex water soluble protein(s) significantly inhibits synthesis of lower molecular weight proteins...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Banerjee A,Emanuel K,Parafina J,Bagchi M

    更新日期:1992-10-01 00:00:00

  • Natural metabolites of 1alpha,25-dihydroxyvitamin D(3) retain biologic activity mediated through the vitamin D receptor.

    abstract::1alpha,25-dihydroxyvitamin D(3) (1alpha,25(OH)(2)D(3)), the active metabolite of vitamin D, mediates many of its effects through the intranuclear vitamin D receptor (VDR, NR1I1), that belongs to the large superfamily of nuclear receptors. Vitamin D receptor can directly regulate gene expression by binding to vitamin D...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Harant H,Spinner D,Reddy GS,Lindley IJ

    更新日期:2000-04-01 00:00:00

  • The detergent solubility properties of a malarial (Plasmodium knowlesi) variant antigen expressed on the surface of infected erythrocytes.

    abstract::Four detergents have been compared for identification of the Plasmodium knowlesi variant antigen on infected erythrocytes by immunoprecipitation analysis. Erythrocytes infected with late trophozoite and schizont forms of cloned asexual parasites were labeled by lactoperoxidase-catalyzed radioiodination and extracted e...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Howard RJ,Barnwell JW

    更新日期:1984-01-01 00:00:00

  • Spreading of mesothelioma cells is rapamycin-sensitive and requires continuing translation.

    abstract::The interaction of cancer cells with extracellular matrix (ECM) is important in metastasization. Here we identified the molecules of the ECM expressed by sarcomatous malignant mesothelioma, and their effect on adhesion and spreading. In addition, by analyzing the relationship between translation and attachment to matr...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Ranzato E,Grosso S,Patrone M,Betta PG,Viarengo A,Biffo S

    更新日期:2009-11-01 00:00:00

  • Cis effect of the type 5 adenovirus E1A gene enhancer element on cellular transformation.

    abstract::Mutants of type 5 adenovirus that lack all or part of the early region 1A (E1A) gene enhancer element transform rodent embryo fibroblast (CREF) cells at higher efficiencies than wild-type virus. An analysis of viral E1A cytoplasmic mRNA levels in mutant and wild-type virus-infected CREF cells revealed no differences i...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Herbst RS,Pelletier M,Babiss LE

    更新日期:1990-01-01 00:00:00

  • Increasing and decreasing protein stability: effects of revertant substitutions on the thermal denaturation of phage lambda repressor.

    abstract::The thermal denaturations of five revertant lambda repressors containing single amino acid substitutions in their N-terminal domains have been studied by differential scanning calorimetry. Two substitutions slightly decrease stability, and the remaining three render the protein more stable than wild type. The Gly48---...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Hecht MH,Hehir KM,Nelson HC,Sturtevant JM,Sauer RT

    更新日期:1985-01-01 00:00:00

  • Soluble 80-kd fragment of cell-CAM 120/80 disrupts cell-cell adhesion.

    abstract::Calcium-dependent cell adhesion molecules (CAMs) mediate intercellular adhesion in epithelial cells and in preimplantation mammalian embryos. One of these molecules, cell-CAM 120/80, is found on cells as a 120-kd membrane glycoprotein and as a soluble 80-kd species in conditioned culture medium [Damsky et al: Cell 34:...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Wheelock MJ,Buck CA,Bechtol KB,Damsky CH

    更新日期:1987-07-01 00:00:00

  • The effects of peptides with estrogen-like activity on cell proliferation and energy metabolism in human derived vascular smooth muscle cells.

    abstract::Hormone replacement therapy (HRT) for post-menopausal symptoms in diabetes is associated with increased risk of coronary heart disease and stroke. Therefore, there is a need for new HRT with no adverse effects on diabetic post-menopausal women. We developed peptides as potential estrogen mimetic compounds and now we e...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Somjen D,Knoll E,Gayer B,Kasher R,Kohen F,Stern N

    更新日期:2010-08-01 00:00:00

  • Identification of an IQGAP1/AKAP79 complex in beta-cells.

    abstract::IQGAP1, is a recently discovered scaffold protein proposed to regulate membrane cytoskeleton events through protein-protein interactions with F-actin, E-cadherin, beta-catenin, and CLIP170. The binding of IQGAP1 to its partners is regulated by calcium/calmodulin (Ca(++)/CaM) and the small molecular weight guanine nucl...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Nauert JB,Rigas JD,Lester LB

    更新日期:2003-09-01 00:00:00

  • Activation of PKR/eIF2α signaling cascade is associated with dihydrotestosterone-induced cell cycle arrest and apoptosis in human liver cells.

    abstract::Androgen receptor (AR) signaling plays an important role in the development and progression of several liver diseases, including hepatocellular carcinoma (HCC) and non-alcoholic fatty liver disease (NAFLD). Dihydrotestosterone (DHT) is the active metabolite of the major circulating androgen, testosterone. In this stud...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Dai R,Yan D,Li J,Chen S,Liu Y,Chen R,Duan C,Wei M,Li H,He T

    更新日期:2012-05-01 00:00:00

  • Ultraviolet radiation (UVR) activates p38 MAP kinase and induces post-transcriptional stabilization of the C/EBPdelta mRNA in G0 growth arrested mammary epithelial cells.

    abstract::The G(0) growth arrest (quiescent) state is highly conserved in evolution to promote survival under adverse environmental conditions. To maintain viability, G(0) growth arrested cells limit gene expression to essential growth control and pro-survival genes. CCAAT enhancer binding protein delta (C/EBPdelta), a member o...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Li B,Si J,DeWille JW

    更新日期:2008-04-01 00:00:00

  • ERK 1/2 signaling pathway is involved in nicotine-mediated neuroprotection in spinal cord neurons.

    abstract::Evidence indicates that agonists of neuronal nicotinic receptors (nAChRs), including nicotine, can induce neuroprotective and anti-apoptotic effects in the CNS. To study these mechanisms, the present study focused on nicotine-mediated modulation of the extracellular regulated kinase 1 and 2 (ERK1/2) pathway in culture...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Toborek M,Son KW,Pudelko A,King-Pospisil K,Wylegala E,Malecki A

    更新日期:2007-02-01 00:00:00

  • The exosomes released from different cell types and their effects in wound healing.

    abstract::Despite important advances in regenerative medicine and tissue engineering, still, wound healing remains a challenging clinical problem. Cell therapy has opened a new viewpoint in medicine as well as wound management, although it has some limitations. On the other hand, there are some hopes for the eliminated of cellu...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Golchin A,Hosseinzadeh S,Ardeshirylajimi A

    更新日期:2018-07-01 00:00:00

  • Transcriptional downregulation of stromelysin by tetracycline.

    abstract::We investigated the role of tetracycline in the transcriptional regulation of matrix metalloproteinases. Using interleukin-1beta (IL-1) induced stromelysin as a model system, we describe the repression of the endogenous stromelysin RNA accumulation, as well as the transcriptional inhibition of various stromelysin prom...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Jonat C,Chung FZ,Baragi VM

    更新日期:1996-03-01 00:00:00

  • Identifying UBA2 as a proliferation and cell cycle regulator in lung cancer A549 cells.

    abstract::Ubiquitin activating enzyme 2 (UBA2) is a basic component of E1-activating enzyme in the SUMOylation system. Expression and function of UBA2 in human cancers are largely unknown. In this study we investigate UBA2 expression the function in human non-small-cell lung cancer. Immunochemistry study showed that UBA2 was ov...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Jiang B,Fan X,Zhang D,Liu H,Fan C

    更新日期:2019-08-01 00:00:00

  • Synthesis and Characterization of Cefotaxime Conjugated Gold Nanoparticles and Their Use to Target Drug-Resistant CTX-M-Producing Bacterial Pathogens.

    abstract::Multidrug-resistance due to "β lactamases having the expanded spectrum" (ESBLs) in members of Enterobacteriaceae is a matter of continued clinical concern. CTX-M is among the most common ESBLs in Enterobacteriaceae family. In the present study, a nanoformulation of cefotaxime was prepared using gold nanoparticles to c...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Shaikh S,Rizvi SMD,Shakil S,Hussain T,Alshammari TM,Ahmad W,Tabrez S,Al-Qahtani MH,Abuzenadah AM

    更新日期:2017-09-01 00:00:00

  • Critical role of the transcription factor AP-1 for the constitutive and interferon-induced expression of IFI 16.

    abstract::IFI 16 is a member of the HIN-200 family of transcriptional regulators that suppress cell growth, modulate the cell cycle and have been linked to cellular differentiation. We hypothesized that the activity of IFI 16 depends on its level of expression and therefore studied the transcriptional activity of the IFI 16 pro...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Clarke CJ,Apostolidis V,Hii LL,Gough DJ,Trapani JA,Johnstone RW

    更新日期:2003-05-01 00:00:00

  • Golgi/granule processing of peptide hormone and neuropeptide precursors: a minireview.

    abstract::Proteolytic processing of precursor proteins is a phylogenetically ancient and widely used mechanism for producing biologically active peptides. Proteolytic cleavage of proproteins begins only after transport to the Golgi apparatus has been completed and in most systems may continue for many hours within newly formed ...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章,评审


    authors: Steiner DF,Docherty K,Carroll R

    更新日期:1984-01-01 00:00:00

  • KRAS mutation and abnormal expression of Cripto-1 as two potential candidate biomarkers for detection of colorectal cancer development.

    abstract::Colorectal cancer (CRC), regardless of standard procedures of treatment and screening, is still considered one of the deadliest cancers in the Western world, and in economically developed Asian countries, especially Iran. The current study was undertaken to investigate whether changes in the level of Cripto-1 (CR-1) e...

    journal_title:Journal of cellular biochemistry

    pub_type: 杂志文章


    authors: Igder S,Mohammadiasl J,Azadpour S,Mansouri E,Ashktorab H,Mokarram P

    更新日期:2020-04-01 00:00:00