309 Works

A nine-hub-gene signature of metabolic syndrome identified using machine learning algorithms and integrated bioinformatics

Guanzhi Liu, Sen Luo, Yutian Lei, Jianhua Wu, Zhuo Huang, Kunzheng Wang, Pei Yang & Xin Huang
Early risk assessments and interventions for metabolic syndrome (MetS) are limited because of a lack of effective biomarkers. In the present study, several candidate genes were selected as a blood-based transcriptomic signature for MetS. We collected so far the largest MetS-associated peripheral blood high-throughput transcriptomics data and put forward a novel feature selection strategy by combining weighted gene co-expression network analysis, protein-protein interaction network analysis, LASSO regression and random forest approaches. Two gene modules and...

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

Shangshang Hu, Jinyan Zhang, Xiaoyu Fang, Guoqing Guo, Jing Dai, Zhiyong Sheng, Dongdong Li, Jiasheng Chen, Li Zhang, Chuanmiao Liu & Yu Gao
Hepatocellular carcinoma (HCC) is a primary liver cancer with high morbidity and mortality. An increasing number of abnormal gene expressions were identified to be associated with the progression of HCC. Previous studies showed that the hsa-miR-30 c-5p (miR-30 c), one of the miR-30 family members, might play a role in suppressing tumor progression in a variety of tumors. The present study aims to examine miR-30 c effects in the development of HCC. The role of...

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

Shangshang Hu, Jinyan Zhang, Xiaoyu Fang, Guoqing Guo, Jing Dai, Zhiyong Sheng, Dongdong Li, Jiasheng Chen, Li Zhang, Chuanmiao Liu & Yu Gao
Hepatocellular carcinoma (HCC) is a primary liver cancer with high morbidity and mortality. An increasing number of abnormal gene expressions were identified to be associated with the progression of HCC. Previous studies showed that the hsa-miR-30 c-5p (miR-30 c), one of the miR-30 family members, might play a role in suppressing tumor progression in a variety of tumors. The present study aims to examine miR-30 c effects in the development of HCC. The role of...

Additional file 2 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

Shiye Sang, Wen Chen, Di Zhang, Xuan Zhang, Wenjing Yang & Changning Liu
Additional file 2. Conserved lncRNAs ratios for each species.

Evidence for the butyrate metabolism as key pathway improving ulcerative colitis in both pediatric and adult patients

Zheng Zhou, Jiasheng Cao, Xiaoming Liu & Mingsong Li
Accumulating evidence has shown many similarities and differences of gene profiles and pathways between pediatric and adult ulcerative colitis (UC) patients. In this study, we aimed to investigate the shared genes and pathways in intestinal tissues of pediatric and adult UC. Differentially expressed genes (DEGs) between pediatric and adult UC were identified via bioinformatic analysis of Gene Expression Omnibus datasets GSE87473 and GSE126124. Gene Ontology and pathway enrichment were used to analyze overlapped and distinguished...

RR3DD: an RNA global structure-based RNA three-dimensional structural classification database

Xu Hong, Jinfang Zheng, Juan Xie, Xiaoxue Tong, Xudong Liu, Qi Song, Sen Liu & Shiyong Liu
The three-dimensional (3D) structure of RNA usually plays an important role in the recognition with RNA-binding protein. Along with the discovering of RNAs, several RNA databases are developed to study the functions of RNA based on sequence, secondary structure, local 3D structural motif and global structure. Based on RNA function and structure, different RNAs are classified and stored in SCOR and DARTS, respectively. The classification of RNA structures is useful in RNA structure prediction and...

Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

Yunjin Zhang, Qingrui Zhao, Shenghan Su, Lingfeng Dan, Xuebei Li, Yu Wang, Yuqing Lin, Zhen Tian, Changhao Sun & Huimin Lu
Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and...

Hypoxia promotes the proliferation of mouse liver sinusoidal endothelial cells: miRNA–mRNA expression analysis

Zhe Qing, Hanfei Huang, Qun Luo, Jie Lin, Shikun Yang, Tao Liu, Zhong Zeng & Tingfeng Ming
During the initial stage of liver regeneration (LR), hepatocytes and liver sinusoidal endothelial cells (LSECs) initiate regeneration in a hypoxic environment. However, the role of LSECs in liver regeneration in hypoxic environments and their specific molecular mechanism is unknown. Therefore, this study aimed to explore the miRNA–mRNA network that regulates the proliferation of LSECs during hypoxia. In this study, first, we found that the proliferation ability of primary LSECs treated with hypoxia was enhanced compared...

A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

Yuxi Gu, Shouyi Tang, Zhen Wang, Luyao Cai, Haosen Lian, Yingqiang Shen & Yu Zhou
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors...

Three periods of gold mineralization in the Liaodong Peninsula, North China Craton

Peng Zhang, Linlin Kou & Yang Zhao
The Liaodong gold province includes voluminous gold deposits, which occur in an Archean gneiss complex, Paleoproterozoic metamorphic rocks, and Mesozoic granite. However, the ore-forming age, the genesis, and the geodynamic setting of the gold deposits are not well constrained. In this study, we have summarized previous geochronology data, H-O-S-Pb isotopes, and He-Ar isotopic compositions of the gold deposits. Based on geochronology data, the gold mineralization was divided into Late Triassic, Early Jurassic, and Early Cretaceous....

Special electromagnetic field-treated water and far-infrared radiation alleviates lipopolysaccharide-induced acute respiratory distress syndrome in rats by regulating haptoglobin

Changyong Luo, Yan Li, Xu Liang, Yifan Chen, Qiao Zou, Yurong Kong, Zhengguang Guo, Wei Sun & Xin Wang
Special electromagnetic field-treated water (SEW) and far-infrared radiation (FIR) can reduce acute respiratory distress syndrome (ARDS) in rats inflicted by lipopolysaccharides (LPSs). However, little is known about its underlying molecular mechanism. Differentially expressed proteins (DEPs) of SEW and FIR interventions were obtained from a proteomics database. A total of 89 DEPs were identified. Enrichment analysis of DEPs was performed using the Database for Annotation, Visualization, and Integrated Discovery. These DEPs were associated with the responses...

Additional file 8 of Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

Menglei Wang, Chenhui Yang, Kangning Wei, Miao Zhao, Liqiang Shen, Jie Ji, Li Wang, Daijing Zhang, Junqiang Guo, Yun Zheng, Juanjuan Yu, Mo Zhu, Haiying Liu & Yong-Fang Li
Additional file 8: Table S5. Sequence of primers used in this study.

Can warnings curb the spread of fake news? The interplay between warning, trust and confirmation bias

Kholekile L. Gwebu, Jing Wang & Ermira Zifla
Despite attempts by social media companies to curb the spread of fake news with warnings flagging news credibility, the effectiveness of such measures remains unclear. Through the lens of the cognitive dissonance theory and individuals’ trust in the news, this study develops a theoretical model that explains why and how warnings affect an individual’s intention to share fake news. The study empirically assesses the predicted relationships using experimental survey data from 382 individuals. The findings...

Can warnings curb the spread of fake news? The interplay between warning, trust and confirmation bias

Kholekile L. Gwebu, Jing Wang & Ermira Zifla
Despite attempts by social media companies to curb the spread of fake news with warnings flagging news credibility, the effectiveness of such measures remains unclear. Through the lens of the cognitive dissonance theory and individuals’ trust in the news, this study develops a theoretical model that explains why and how warnings affect an individual’s intention to share fake news. The study empirically assesses the predicted relationships using experimental survey data from 382 individuals. The findings...

Identification of downstream targets and signaling pathways of long non-coding RNA NR_002794 in human trophoblast cells

Yinyao Ma, Hua Wu, Xuxia Liang, Chun Zhang, Yanhua Ma, Yanfen Wei, Jing Li & Hui Chen
Preeclampsia (PE) is a huge threat to pregnant women. Our previous study demonstrated that long non-coding RNA (lncRNA) NR_002794 was highly expressed in placentas of PE patients and could regulate the phenotypes of trophoblast cells. However, the downstream regulatory mechanisms of NR_002794 remain unknown. In this text, some potential downstream targets or signaling pathways of NR_002794 were identified through RNA sequencing (RNA-seq) and bioinformatics analysis in SWAN71 trophoblast cells. Western blot assay demonstrated that NR_002794...

Identification of hsa_circ_0002024 as a prognostic competing endogenous RNA (ceRNA) through the hsa_miR_129-5p/Anti-Silencing Function 1B Histone Chaperone (ASF1B) axis in renal cell carcinoma

Zhe Chen, Dehua Ou, Zhuangkai Huang & Peilin Shen
We aimed to identify novel circular RNAs (circRNAs) as prognostic competing endogenous RNAs (ceRNAs) to serve as genetic biomarkers and therapeutic targets for renal cell carcinoma (RCC). High-throughput sequencing data of circRNAs from Gene Expression Omnibus (GEO) and of microRNAs (miRNAs) and messenger RNAs (mRNAs) from The Cancer Genome Atlas (TCGA) were retrieved to identify differentially expressed RNAs (DERNAs). DEmRNAs were subjected to weighted gene coexpression network analysis (WGCNA) to identify prognostic DEmRNA (proDEmRNA) modules....

B7 family member H4 induces epithelial-mesenchymal transition and promotes the proliferation, migration and invasion of colorectal cancer cells

Yuzhen Yin, Lili Shi, Jing Yang, Hui Wang, Hang Yang & Qiang Wang
Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, which has the second highest incidence among gastrointestinal tumors. At present, due to the limitations of current CRC treatment strategies, there is an urgent need for developing more effective therapies. B7 family member H4 (B7-H4) is associated with the progression of a wide spectrum of cancers, but its functional role in CRC is unknown. The purpose of this study is to clarify the role...

Sweeping analysis of transcript profile in dengue virus serotype 3 infection and antibody-dependent enhancement of infection

Mingwang Long, Yue Pan, Junying Chen, Fan Jia, Han Wang, Daiying Li, Kai Feng, Lingmei Yan, Xiaodan Wang, Xuelei Ning, Lijuan Qiu, Juan Zhang & Qiangming Sun
Dengue virus infection mainly causes dengue hemorrhagic fever (DHF) and/or dengue shock syndrome (DSS). However, ADE (antibody-dependent enhancement) is one of the main pathogenic factors, and its pathogenic mechanism has not been fully elucidated. Recently, with the development of high-throughput sequencing, an increased number of RNAs have been confirmed to play a vital regulatory role in the process of virus infection. However, there is a lack of research on dengue virus infection and ADE. In...

Rapid humoral immune responses are required for recovery from haemorrhagic fever with renal syndrome patients

Yaoni Li, Chuansong Quan, Weijia Xing, Peihan Wang, Jiming Gao, Zhenjie Zhang, Xiaolin Jiang, Chuanmin Ma, Michael J. Carr, Qian He, Lei Gao, Yuhai Bi, Hua Tang & Weifeng Shi
Haemorrhagic fever with renal syndrome (HFRS) following Hantaan virus (HTNV) infection displays variable clinical signs. Humoral responses elicited during HTNV infections are considered important, however, this process remains poorly understood. Herein, we have investigated the phenotype, temporal dynamics, and characteristics of B-cell receptor (BCR) repertoire in an HFRS cohort. The serological profiles were characterized by a lowered expression level of nucleoprotein (NP)-specific antibody in severe cases. Importantly, B-cell subsets were activated and proliferated within the...

Transcriptome profiling revealed heat stress-responsive genes in Arabidopsis through integrated bioinformatics analysis

Meili Guo, Xin Liu, Jiahui Wang, Yusu Jiang, Jinhuan Yu & Jing Gao
Heat stress is an environmental challenge that reduces plant productivity and growth. Plants have developed corresponding mechanisms to survive this adverse environmental stress. To demonstrate the mechanisms of how plants adapt to the environmental challenge, the heat response experiments involving Arabidopsis thaliana were retrieved from the GEO database. After quantile normalization of the GEO raw data, the differentially expressed genes (DEGs) in response to heat stress were identified by robust rank aggregation (RRA) algorithm, including...

Downregulation of Smad4 expression confers chemoresistance against imatinib mesylate to chronic myeloid leukemia K562 cells

Jiangzhao Zhang, Min Zhang, Yan Liang, Min Liu & Zhiping Huang
Objective: Imatinib mesylate (IM), a tyrosine kinase inhibitor, exhibits clinically prominent effects against chronic myeloid leukemia (CML); however, a few patients have shown resistance to IM treatment, resulting in disease progression. Smad4 is a tumor inhibitor that transduces TGF-β signaling and modulates genomic stability. Previous studies have indicated that decreased Smad4 expression played a bidirectional role in chemosensitivity in many types of cancers. Therefore, this study aims to evaluate the association between IM sensitivity and...

A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

Yuxi Gu, Shouyi Tang, Zhen Wang, Luyao Cai, Haosen Lian, Yingqiang Shen & Yu Zhou
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors...

A seven-gene signature and the C–C motif chemokine receptor family genes are the sarcoma-related immune genes

Jiarui Chen, Tuo Liang, Jiemei Cen, Jie Jiang, Shixin Pan, Shengsheng Huang, Liyi Chen, Xuhua Sun, Hao Li, Tianyou Chen, Wei Liang, Shian Liao, Chaojie Yu, Yuanlin Yao, Zhen Ye, Wuhua Chen, Hao Guo, Xinli Zhan & Chong Liu
Cells of the tumor microenvironment exert a vital influence on sarcoma prognosis. This study aimed to analyze and identify differentially expressed genes (DEGs) related to immunity and their significance as immune biomarkers for the accurate prediction of overall survival of patients with sarcoma. The Cancer Genome Atlas was adopted for obtaining sarcoma gene microarray and corresponding clinical information. ESTIMATE algorithm was used to calculate tumor immune microenvironment indices. Immune-associated DEGs were identified using the limma...

Identification and validation of seven RNA binding protein genes as a prognostic signature in oral cavity squamous cell carcinoma

Zijing Huang, Tianjun Lan, Junjie Wang, Zhifeng Chen & Xiaolei Zhang
RNA binding proteins (RBPs) play a pivotal role in various biological processes, and aberrant expression of RBPs is closely associated with tumorigenesis and progression. However, the role of RBPs in oral cavity squamous cell carcinoma (OCSCC) is yet unveiled. In this study, RNA sequences and clinical information of OCSCC samples were acquired from The Cancer Genome Atlas (TCGA) database. A total of 650 RBPs, with significantly different expression between healthy and OCSCC samples, were identified...

A novel pyroptosis-related lncRNA signature for prognostic prediction in patients with lung adenocarcinoma

Jiahang Song, Yuanyuan Sun, Hui Cao, Zhengcheng Liu, Lei Xi, Changqing Dong, Rusong Yang & Ye Shi
Lung adenocarcinoma (LUAD) has been the major cause of tumor-associated mortality in recent years and has a poor prognosis. Pyroptosis is regulated via the activation of inflammasomes and participates in tumorigenesis. However, the effects of pyroptosis-related lncRNAs (PRlncRNAs) on LUAD have not yet been completely elucidated. Therefore, we attempted to systematically explore patterns of cell pyroptosis to establish a novel signature for predicting LUAD survival. Based on TCGA database, we set up a prognostic model...

Registration Year

  • 2021
    309

Resource Types

  • Dataset
    309

Affiliations

  • Chinese Academy of Medical Sciences & Peking Union Medical College
    309
  • Shanghai Jiao Tong University
    191
  • Fudan University
    182
  • Sun Yat-sen University
    169
  • Zhejiang University
    166
  • Huazhong University of Science and Technology
    165
  • Capital Medical University
    165
  • Sichuan University
    163
  • Chinese Academy of Sciences
    153
  • Peking University
    145