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Genome-wide identification,evolution,and expression profiling of bHLH transcription factor family in response to abiotic stresses in pearl millet(Pennisetum glaucum L.) 认领 引用
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作者 Atiqa Najeeb Rezwan Tariq +6 位作者 Ammara Hussain Muhammad Jawad Hassan Usama Khalid Haidong Yan Zhong Yun Zheni Xie Linkai Huang 《Grass Research》 2025年第1期49-63,共15页
Pearl millet(Pennisetum glaucum L.)is a highly valuable crop for food,fodder,and biofuel production;however,its productivity is significantly hindered byvarious abiotic stresses.It is one of the most functionally vers... Pearl millet(Pennisetum glaucum L.)is a highly valuable crop for food,fodder,and biofuel production;however,its productivity is significantly hindered byvarious abiotic stresses.It is one of the most functionally versatile and expansive transcription factor(TF)families in plants.The basic helix-loop-helix(bHLH)plays an imperative role in regulating responses under environmental stresses.Therefore,by using phylogenetic analysis,this study identified 110 PgbHLHTFs and broadly classified them into 12 subfamilies with 20 conserved motifs.The structural analysis illustrated that PgbHLHs proteins within each subgroupwere relatively conserved.Chromosomal mapping revealed the distribution of PgbHLH genes across all seven chromosomes of pearl millet.Evolutionaryanalysis of pearl millet with Arabidopsis thaliana(145 AtbHLH genes)and Oryza sativa(139 OsbHLH genes)revealed distinct orthologous and paralogousgenes,facilitating gene functions prediction in reference species.Collinearity analysis showed both the conservation of PgbHLH genes across multiple plantspecies and their collinear divergence based on gene order and similarity metrics,providing valuable insights into the functional evolution of this genefamily.Additionally,putative cis-regulatory element(CRE)analysis of the PgbHLH promoters revealed a diverse range of regulatory elements,with stressresponsiveCREs accounting for 34%of all identified elements.Moreover,in-silico expression profiling of PgbHLH genes in leaf and root tissues under heat,drought,and salt stress conditions demonstrated their diverse regulatory roles in abiotic stress responses.This study provides a valuable resource for futurefunctional validation studies aimed at improving abiotic stress resilience in pearl millet through molecular breeding. 展开更多
关键词 regulating responses transcription factor tf families expression profiling phylogenetic analysisthis genome wide identification abiotic stresses pearl millet pennisetum bhlh transcription factor family
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Genome-Wide Gene Expression Profiling in Human Adipose-Derived Mesenchymal Stem Cells 认领 引用
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作者 Sae Hee Cheon Sung-Whan Kim 《BIOCELL》 SCIE 2025年第9期1697-1710,共14页
Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyz... Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis. 展开更多
关键词 Adipose-derived mesenchymal stem cells angiogenesis extracellular matrix gene expression profiling immune modulation
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Identification,bioinformatic analysis and expression profiling of candidate mRNA-like non-coding RNAs in Sus scrofa 认领 引用 被引量：9
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作者 Bang Xiao Xingju Zhang +6 位作者 Yong Li Zhonglin Tang Shulin Yang Yulian Mu Wentao Cui Hong Ao Kui Li 《Journal of Genetics and Genomics》 SCIE CAS 2009年第12期695-702,共8页
Messenger RNA-like non-coding RNAs （mlncRNAs） are a newly identified group of non-coding RNAs （ncRNAs） that may be involved in a number of critical cellular events. In this study, 93 candidate porcine mlncRNAs wer... Messenger RNA-like non-coding RNAs （mlncRNAs） are a newly identified group of non-coding RNAs （ncRNAs） that may be involved in a number of critical cellular events. In this study, 93 candidate porcine mlncRNAs were obtained by computational prediction and screening, among which 72 were mapped to the porcine genome. Further analysis of 8 representative candidates revealed that these mlncRNA candidates are not highly conserved among species. Remarkably, one of the candidates, sTF35495, was found to be precursor of a putative porcine microRNA. By RACE PCR, we determined that the full length of sTF35495 was 3 kb. The protein-coding potential of this RNA was tested in silico with no significant finding. Semi-quantitative RT-PCR analysis of the subgroup of 8 candidates revealed two distinct expression profiles and two molecules were further validated by real-time PCR. The predicted pre-microRNA sequence in this study provides a potentially interesting insight into the in vivo function of porcine mlncRNAs and our findings suggest that they play key biological roles in Sus scrofa. 展开更多
关键词 putative porcine mlncRNA chromosome localization interspecies conservation pre-microRNA RACE expression profiling qPCR
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Gene expression profiling of the rat sciatic nerve in early Wallerian degeneration after injury 认领 引用 被引量：7
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作者 Dengbing Yao Meiyuan Li +4 位作者 Dingding Shen Fei Ding Shibi Lu Qin Zhao Xiaosong Gu 《Neural Regeneration Research》 SCIE CAS CSCD 2012年第17期1285-1292,共8页
Wallerian degeneration is an important area of research in modern neuroscience. A large number of genes are differentially regulated in the various stages of Wallerian degeneration, especially during the early respons... Wallerian degeneration is an important area of research in modern neuroscience. A large number of genes are differentially regulated in the various stages of Wallerian degeneration, especially during the early response. In this study, we analyzed gene expression in early Wallerian degeneration of the distal nerve stump at 0, 0.5, 1,6, 12 and 24 hours after rat sciatic nerve injury using gene chip microarrays. We screened for differentially-expressed genes and gene expression patterns. We examined the data for Gene Ontology, and explored the Kyoto EncycLopedia of Genes and Genomes Pathway. This allowed us to identify key regulatory factors and recurrent network motifs. We identified 1 546 differentially-expressed genes and 21 distinct patterns ofgene expression in early Wallerian degeneration, and an enrichment of genes associated with the immune response, acute inflammation, apoptosis, cell adhesion, ion transport and the extracellular matrix. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed components involved in the Jak-STAT, ErbB, transforming growth factor-13, T cell receptor and calcium signaling pathways. Key factors included interleukin-6, interleukin-1, integrin, c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine （C-C motif） ligand, matrix metalloproteinase, BH3 interacting domain death agonist, baculoviral lAP repeat-containing 3 and Rac. The data were validated with real-time quantitative PCR. This study provides a global view of gene expression profiles in eady Wallerian degeneration of the rat sciatic nerve. Our findings provide insight into the molecular mechanisms underlying early Wallerian degeneration, and the regulation of nerve degeneration and regeneration. 展开更多
关键词 Wallerian degeneration sciatic nerve microarrays expression profiling rats neural regeneration
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Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling 认领 引用 被引量：9
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作者 Yue-Zheng Zhang Lian-Hai Zhang +8 位作者 Yang Gao Chao-Hua Li Shu-Qinjia Ni Liu Feng Cheng De-Yun Niu William CS Cho Jia-Fu Ji Chang-Qing Zeng 《World Journal of Gastroenterology》 SCIE CAS CSCD 2011年第13期1710-1717,共8页
AIM: To develop a prognostic gene set that can predict patient overall survival status based on the whole genome expression analysis. METHODS: Using Illumina HumanWG-6 BeadChip followed by semi-supervised analysis, we... AIM: To develop a prognostic gene set that can predict patient overall survival status based on the whole genome expression analysis. METHODS: Using Illumina HumanWG-6 BeadChip followed by semi-supervised analysis, we analyzed the expression of 47 296 transcripts in two batches of gastric cancer patients who underwent surgical resection. Thirty-nine samples in the first batch were used as the training set to discover candidate markers correlated to overall survival, and thirty-three samples in the second batch were used for validation. RESULTS: A panel of ten genes were identified as prognostic marker in the first batch samples and classified patients into a lowand a high-risk group with significantly different survival times (P = 0.000047). This prognostic marker was then verified in an independent validation sample batch (P = 0.0009). By comparing with the traditional Tumor-node-metastasis (TNM) staging system, this ten-gene prognostic marker showed consistent prognosis results. It was the only independent prognostic value by multivariate Cox regression analysis (P = 0.007). Interestingly, six of these ten genes are ribosomal proteins, suggesting a possible association between the deregulation of ribosome related gene expression and the poor prognosis. CONCLUSION: A ten-gene marker correlated with overall prognosis, including 6 ribosomal proteins, was identified and verified, which may complement the predictive value of TNM staging system. 展开更多
关键词 Gastric cancer Gene expression profiling Survival markers Prognosis Ribosomal proteins
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Identification of biomarkers of human pancreatic adenocarcinomas by expression profiling and validation with gene expression analysis in endoscopic ultrasound-guided fine needle aspiration samples 认领 引用 被引量：6
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作者 Henrik Laurell Michèle Bouisson +7 位作者 Philippe Berthelémy Philippe Rochaix Sébastien Déjean Philippe Besse Christiana Susini Lucien Pradayrol Nicole Vaysse Louis Buscail 《World Journal of Gastroenterology》 SCIE CAS 2006年第21期3344-3351,共8页
AIM： To compare gene expression profiles of pancreatic adenocarcinoma tissue specimens, human pancreatic and colon adenocarcinoma and leukemia cell lines and normal pancreas samples in order to distinguish differenti... AIM： To compare gene expression profiles of pancreatic adenocarcinoma tissue specimens, human pancreatic and colon adenocarcinoma and leukemia cell lines and normal pancreas samples in order to distinguish differentially expressed genes and to validate the differential expression of a subset of genes by quantitative real-time RT-PCR （RT-QPCR） in endoscopic ultrasound-guided fine needle aspiration （EUS-guided FNA） specimens.METHODS： Commercially dedicated cancer cDNA macroarrays （Atlas Human Cancer 1.2） containing 1176 genes were used. Different statistical approaches （hierarchical clustering, principal component analysis （PCA） and SAM） were used to analyze the expression data. RT-QPCR and immunohistochemical studies were used for validation of results.RESULTS： RT-QPCR validated the increased expression of LCN2 （lipocalin 2） and for the first time PLAT （tissue-type plasminogen activator or tPA） in malignant pancreas as compared with normal pancreas. Immunohistochemical analysis confirmed the increased expression of LCN2 protein localized in epithelial cells of ducts invaded by carcinoma. The analysis of PLAT and LCN2 transcripts in 12 samples obtained through EUS-guided FNA from patients with pancreatic adenocarcinoma showed significantly increased expression levels in comparison with those found in normal tissues, indicating that a sufficient amount of high quality RNA can be obtained with this technique.CONCLUSION： Expression profiling is a useful method to identify biomarkers and potential target genes. Molecular analysis of EUS-guided FNA samples in pancreatic cancer appears as a valuable strategy for the diagnosis of pancreatic adenocarcinomas. 展开更多
关键词 Pancreas Colon Adenocarcinoma Gene expression profiling Endoscopic ultrasonography Ultrasound Fine needle aspiration
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Gene expression profiling of Puccinia striiformis f.sp.tritici during development reveals a highly dynamic transcriptome 认领 引用 被引量：5
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作者 Xueling Huang Xianming Chen +2 位作者 Tristan Coram Meinan Wang Zhensheng Kang 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2011年第8期357-371,共15页
Puccinia striiformis f. sp. tritici （PsO causes stripe rust, one of the most important diseases of wheat worldwide, cDNA libraries had been constructed from urediniospores, germinated urediniospores and haustoria. Ho... Puccinia striiformis f. sp. tritici （PsO causes stripe rust, one of the most important diseases of wheat worldwide, cDNA libraries had been constructed from urediniospores, germinated urediniospores and haustoria. However, little is known about the expression patterns of the genes related to the infection process and sporulation of the pathogen. In this study, a custom oligonucleotide microarray was constructed using sequences of 442 gene transcripts selected from Pst cDNA libraries. The expression patterns of the genes were determined by hybridizing the microarray with cDNA from Pst in vitro and Pst-infected wheat leaves. The time course study identified 55 transcripts that were differentially expressed during the infection process in a compatible interaction. They were identified to have functions related to the following biological processes, including carbohydrate and lipid metabolism, energy, cell signaling, protein synthesis, cell structure and division. In an incompatible interaction, 17 transcripts of the pathogen were differentially expressed in resistant wheat leaves inoculated with an avirulent Pst race, ten of which had similar expression patterns to those in the compatible interaction. Several candidates for pathogenicity and virulence/avirulence related genes were also identified. The results of quantitative real-time PCR validated the expression patterns of some selected genes. The study demonstrates that the custom oligonucleotide microarray technology is useful to determine the expression patterns of the pathogen genes involved in different types of the host--pathogen interactions and stages of development. 展开更多
关键词 Puccinia striifonnis Stripe rust Yellow rust Expression profiling Microarray Wheat
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Gene and protein expression profiling analysis of young spike development in large spike wheat germplasms 认领 引用 被引量：1
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作者 CHEN Dan ZHANG Jin-peng +5 位作者 LIU Wei-hua WU Xiao-yang YANG Xin-ming LI Xiu-quan LU Yu-qing LI Li-hui 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2016年第4期744-754,共11页
The wheat grain number per spike （GNPS） is a major yield-limiting factor in wheat-breeding programs. Germplasms with a high GNPS are therefore valuable for increasing wheat yield potential. To investigate the molecu... The wheat grain number per spike （GNPS） is a major yield-limiting factor in wheat-breeding programs. Germplasms with a high GNPS are therefore valuable for increasing wheat yield potential. To investigate the molecular characteristics of young spike development in large-spike wheat germplasms with high GNPS, we performed gene and protein expression profiling analysis with three high-GNPS wheat lines （Pubing 3228, Pubing 3504 and 4844-12） and one Iow-GNPS control variety （Fukuho）. The phenotypic data for the spikes in two growth seasons showed that the GNPS of the three large-spike wheat lines were significantly higher than that of the Fukuho control line. The Affymetrix wheat chip and isobaric tags for relative and absolute quantitation-tandam mass spectrometry （iTRAQ-MS/MS） technology were employed for gene and protein expression profiling analyses of young spike development, respectively, at the floret primordia differentiation stage. A total of 598 differentially expressed transcripts （270 up-regulated and 328 down-regulated） and 280 proteins （122 up- regulated and 158 down-regulated） were identified in the three high-GNPS lines compared with the control line. We found that the expression of some floral development-related genes, including Wknoxlb, the AP2 domain protein kinase and the transcription factor HUA2, were up-regulated in the high-GNPS lines. The expression of the SHEPHERD （SHD） gene was up-regulated at both the transcript and protein levels. Overall, these results suggest that multiple regulatory pathways, including the CLAVATA pathway and the meristem-maintaining KNOX protein pathway, take part in the development of the high-GNPS phenotype in our wheat germplasms. 展开更多
关键词 wheat high grain number per spike spike development expression profiling
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Comprehensive genomic analysis and expression profiling of cysteine-rich polycomb-like transcription factor gene family in tea tree 认领 引用 被引量：7
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作者 Hong Nan Yanglei Lin +1 位作者 Xinghua Wang Lizhi Gao 《Horticultural Plant Journal》 SCIE CAS CSCD 2021年第5期469-478,共10页
Cysteine-rich polycomb-like(CPP)is a small gene family in plants,which plays key role in plant development and stress response.Although CPP transcription factors have been characterized in several other plant species,... Cysteine-rich polycomb-like(CPP)is a small gene family in plants,which plays key role in plant development and stress response.Although CPP transcription factors have been characterized in several other plant species,a genome-wide characterization of the CPP gene family has been absent in Camellia sinensis.In this study,we totally identified 7,8,and 8 non-redundant CsCPP genes in three published genomes,including Camellia sinensis var.assamica cv.Yunkang-10(CSA-YK10),Camellia sinensis var.sinensis cv.Biyun(CSS-BY)and Camellia sinensis var.sinensis cv.Shuchazao(CSS-SCZ).CPP proteins from tea tree and other plant species were classified into three groups,which were further divided into four subgroups based on phylogenetic relationships.Most CPP genes in the same subgroup had similar gene structures and conserved motifs.The cis-acting elements analysis indicated that CPP genes might be involved in plant growth,development and stress responses.Analysis of gene expression using qRT-PCR experiments validated that CPP genes exhibited different expression patterns across the examined tissues.All the genes were expressed differentially in a range of tissues,indicating that CPPs were involved in a range of developmental and physiological processes.This study has obtained new insights into the evolution and function of the CPP gene family in the growth and development of tea plants,and also provide candidate genes for further functional characterization in tea tree. 展开更多
关键词 Camellia sinensis CPP transcription factor Genome-wide analysis Gene expression profiling
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Genome-wide identification and expression profiling of MYB transcription factor genes in radish(Raphanus sativus L.) 认领 引用 被引量：3
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作者 Everlyne M'mbone WIULEKE WANG Yan +7 位作者 ZHANG Wan-ting XU Liang YING Jia-li Bernard K.KARANJA ZHU Xian-wen FAN Lian-xue Zarwali AHMADZAI LIU Li-wang 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2021年第1期120-131,共12页
Radish(Raphanus sativus L.), an important root vegetable crop of the Brassicaceae family, has a high level of anthocyanin accumulation in its pigment root tissues. It was reported that MYB transcription factors(TFs) p... Radish(Raphanus sativus L.), an important root vegetable crop of the Brassicaceae family, has a high level of anthocyanin accumulation in its pigment root tissues. It was reported that MYB transcription factors(TFs) play vital roles in plant development and anthocyanin metabolism, and the PAP1/2 could promote expression of anthocyanin biosynthesis genes. In this study, a total of 187 radish MYB genes(Rs MYBs) were identified in the radish genome and clustered into 32 subfamilies. Among them, 159 Rs MYBs were localized on nine radish chromosomes. Interestingly, 14 Rs MYBs exhibited differential expression profiles in different taproot developmental stages among four differently colored radish lines. A number of Rs MYBs were highly expressed in the pigmented root tissues at the maturity stage, several genes including Rs MYB41, Rs MYB117, and Rs MYB132 being homologous to PAP1/2, showed high expression levels in the red skin of NAU-YH(red skin-white flesh) taproot, while Rs MYB65 and Rs MYB159 were highly expressed in the purple root skin of NAU-YZH(purple skin-red flesh), indicating that these Rs MYBs might positively regulate the process of anthocyanin accumulation in radish taproot. These results would provide valuable information for further functional characterization of Rs MYBs, and facilitate clarifying the molecular mechanism underlying anthocyanin biosynthesis in radish. 展开更多
关键词 radish MYB transcription factors anthocyanin biosynthesis expression profiling
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Gene expression profiling defined pathways correlated with fibroblast cell proliferation induced by Opisthorchis viverrini excretory /secretory product 认领 引用 被引量：5
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作者 Chanitra Thuwajit Peti Thuwajit +4 位作者 Kazuhiko Uchida Daoyot Daorueang Sasithorn Kaewkes Sopit Wongkham Masanao Miwa 《World Journal of Gastroenterology》 SCIE CAS 2006年第22期3585-3592,共8页
AIM： To investigate the mechanism of fibroblast cell proliferation stimulated by the Opisthorchis viverrini excretory/secretory （ES） product. METHODS： NIH-3T3, mouse fibroblast cells were treated with O. viverrini... AIM： To investigate the mechanism of fibroblast cell proliferation stimulated by the Opisthorchis viverrini excretory/secretory （ES） product. METHODS： NIH-3T3, mouse fibroblast cells were treated with O. viverrini ES product by non-contact co-cultured with the adult parasites. Total RNA from NIH-3T3 treated and untreated with O. viverrini was extracted, reverse transcribed and hybridized with the mouse 15K complementary DNA （cDNA） array. The result was analyzed by ArrayVision version 5 and GeneSpring version 5 softwares. After normalization, the ratios of gene expression of parasite treated to untreated NIH-3T3 cells of 2-and more-fold upregulated was defined as the differentially expressed genes. The expression levels of the signal transduction genes were validated by semiquantitative SYBR-based real-time RT-PCR. RESULTS： Among a total of 15 000 genes/ESTs, 239 genes with established cell proliferation-related function were 2 fold-and more-up-regulated by O. viverrini ES product compared to those in cells without exposure to the parasitic product. These genes were classified into groups including energy and metabolism, signal transduction, protein synthesis and translation, matrix and structural protein, transcription control, cell cycle and DNA replication. Moreover, the expressions of serinethreonine kinase receptor, receptor tyrosine kinase and collagen production-related genes were up-regulated by O.viverrini ES product, The expression level of signal transduction genes, pkC, pdgfra, jak 1, eps 8, tgfβ 1/4,strap and h ras measured by real-time RT-PCR confirmed their expression levels to those obtained from cDNA array. However, only the up-regulated expression of pkC,eps 8 and tgfβ3 1/4 which are the downstream signaling molecules of either epidermal growth factor （EGF） or transforming growth factor-β （TGF-β） showed statistical significance （P 〈 0.05）.CONCLUSION： O. viverrini ES product stimulates the significant changes of gene expression in several functional categories and these mainly include transcripts related to cell proliferation. The TGF-β and EGF signal transduction pathways are indicated as the possible pathways of O. viverrini-driven cell proliferation. 展开更多
关键词 Gene expression profile Opisthorchis viverrini Excretory/secretory product cDNA array Fibroblast Cell proliferation Signal transduction Cholangiocarcinogenesis
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GENE EXPRESSION PROFILING OF HUMAN PROMYELOCYTIC LEUKEMIA HL-60 CELL TREATED BY AJOENE 认领 引用 被引量：6
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作者 方志俊 黄文秀 +4 位作者 黄明辉 梁润松 崔景荣 王夔 杨梦苏 《Chinese Journal of Cancer Research》 CAS 2002年第1期11-17,共7页
Objective: Ajoene, a major compound extracted from crashed garlic, has been shown to have antitumor, antimycotic, antimicrobial, antimutagenic functions in vivo or in vitro and treated as a potential antitumor drug. H... Objective: Ajoene, a major compound extracted from crashed garlic, has been shown to have antitumor, antimycotic, antimicrobial, antimutagenic functions in vivo or in vitro and treated as a potential antitumor drug. However, the molecular mechanisms underlying the tumor cytotoxicity of ajoene and even garlic substances are poorly defined. In the present study, we aimed to generate gene expression profiles of HL-60 cell treated by ajoene. Methods: A cDNA microarray presenting 2400 of genes amplified from human leukocyte cDNA library was constructed and the gene expression profiles of HL-60 cell induced by ajoene were generated. Results: After data analysis, 28 differentially expressed genes were identified and sequenced. These genes include 21 known genes and 7 ESTs. Most of the known genes are related to cell apoptosis, such as secretory granule (PRG1), beta-2 microglobulin (B2M), 16S ribosomal RNA gene and ribosomal protein S12. Several genes are related to cell differentiation, including the genes similar to H3 histone and ribosomal protein L31. Northern blot analysis was used to verify and quantify the expression of selected genes. Conclusion: Ajoene can induce HL-60 cell apoptosis significantly and may play a role in differentiation. cDNA microarray technology can be a valuable tool to gain insight into molecular events of pharmacological mechanism of herbal medicine. 展开更多
关键词 Ajoene cDNA microarray cDNA Gene expression profiles
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Discovery of molecular associations among aging, stem cells, and cancer based on gene expression profiling 认领 引用 被引量：1
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作者 Xiaosheng Wang 《Chinese Journal of Cancer》 2013年第4期155-161,共7页
The emergence of a huge volume of "omics" data enables a computational approach to the investigation of the biology of cancer. The cancer informatics approach is a useful supplement to the traditional experi... The emergence of a huge volume of "omics" data enables a computational approach to the investigation of the biology of cancer. The cancer informatics approach is a useful supplement to the traditional experimental approach. I reviewed several reports that used a bioinformatics approach to analyze the associations among aging, stem cells, and cancer by microarray gene expression profiling. The high expression of aging- or human embryonic stem cell-related molecules in cancer suggests that certain important mechanisms are commonly underlying aging, stem cells, and cancer. These mechanisms are involved in cell cycle regulation, metabolic process, DNA damage response, apoptosis, p53 signaling pathway, immune/inflammatory response, and other processes, suggesting that cancer is a developmental and evolutional disease that is strongly related to aging. Moreover, these mechanisms demonstrate that the initiation, proliferation, and metastasis of cancer are associated with the deregulation of stem cells. These findings provide insights into the biology of cancer. Certainly, the findings that are obtained by the informatics approach should be justified by experimental validation. This review also noted that next-generation sequencing data provide enriched sources for cancer informatics study. 展开更多
关键词 Cancer aging stem cells gene expression profiling Cancer informatics
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GENE EXPRESSION PROFILING OF GANGLIOGLIOMA MALIGNANT PROGRESSION BY cDNA ARRAY 认领 引用
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作者 张全斌 黄强 +4 位作者 董军 王爱东 孙继勇 兰青 胡庚熙 《Chinese Journal of Cancer Research》 CAS 2005年第1期11-16,共6页
Objective: To establish gene expression profiles associated with malignant progression of ganglioglioma. Methods: The primary and two recurrent glioma specimens were collected intraoperatively from the same patient wh... Objective: To establish gene expression profiles associated with malignant progression of ganglioglioma. Methods: The primary and two recurrent glioma specimens were collected intraoperatively from the same patient who experienced tumor transformation into anaplastic astrocytoma and glioblastoma multiform for the first and second recurrence respectively. Gene expression was assayed through cDNA array and bioinformatics analysis. Results: A total of 197 differentially expressed genes with differential ratio value more than 3 compared with normal brain tissue were obtained. Among 109 functionally denned genes, those associated with development ranked the first by frequency, followed by genes associated with metabolism, differentiation, signal transduction and so on. As a result of cluster analysis among 368 genes, eleven genes were up regulated with malignant progression, while six genes were down regulated. Conclusion: Gene expression profiles associated with malignant progression of glioma were successfully established, which provides a powerful tool for research on molecular mechanisms of malignant progression of gliomas. 展开更多
关键词 cDNA microarray Glioma Gene expression profile Malignant progression
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Expression Profiling of Hereditary versus Sporadic Prostate Cancer Suggests CYR61, EGR3, KLF6 and SNF1LK as Differentially Expressed Genes 认领 引用
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作者 Diem Nguyen Bentzon Martin Morck Mortensen +2 位作者 Torben Orntoft Lars Dyrskjot Michael Borre 《Open Journal of Urology》 2012年第2期55-66,共12页
Background: Distinguishing between sub-clinical and aggressive forms of prostate cancer is difficult due to the heterogeneity of the disease. It is, however, important to identify aggressive forms to guide proper trea... Background: Distinguishing between sub-clinical and aggressive forms of prostate cancer is difficult due to the heterogeneity of the disease. It is, however, important to identify aggressive forms to guide proper treatment. This study compared gene expression profiles in cancer cells from hereditary and sporadic prostate cancer cases and attempted to correlate differentially regulated genes with clinico-pathological characteristics and prognosis. Materials and methods: The study population comprised patients diagnosed with clinically localized prostate cancer undergoing prostatectomy. Patients were divided into hereditary and sporadic cancer cases based on their family history. Fresh frozen biopsies from prostatectomy specimens were laser-dissected for RNA-extraction. Affymetrix HG-U133 Plus GeneChips were used to measure gene expression loaded onto Cluster 3.0 and Ingenuity Pathway Analysis softwares to examine the relationship among genes between groups. Differentially expressed genes were selected for protein expression analysis using immunohistochemistry on histological sections and tissue microarrays. Results: No single genes were signifycantly differentially expressed between hereditary and sporadic cases after adjustment for multiple testing. Using cluster analysis, four transcripts were found to be upregulated in hereditary prostate cancer tissue: CYR61, EGR3, KLF6 and SNF1LK. The intensity of CYR61, EGR2, KLF6 and SNF1LK immunostainings, however, were not significantly different in a separate sample of hereditary and sporadic prostate cancers. Furthermore, no correlations between CYR61, EGR2, KLF6, and SNF1LK staining intensities and the clinico-pathological variables or disease-free survival were detected, except for EGR3 that was significantly associated with T stage (p = 0.04). Conclusion: Overall, no single transcript level was significantly associated with hereditary prostate cancer. Cluster analysis suggested that the expression of CYR61, EGR3, KLF6 and SNF1LK were upregulated in cancer tissue from hereditary cases, but we were not able to confirm this on the protein level, and levels of these proteins were not found to correlate with clinico-pathological characteristics or biochemical recurrence. 展开更多
关键词 Hereditary Prostate Cancer Microarray Expression Profile Immunohistochemistry Radical Prostatectomy Tissue Microarray
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Gene Expression Profiling of the Mouse Pancreas during the Secondary Transition in the Organogenesis of the Pancreatic Gland* 认领 引用
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作者 Stefanie J. Willmann 《Journal of Diabetes Mellitus》 CAS 2021年第1期1-9,共9页
Diabetes mellitus is a chronic disease that impacts the homeostasis of blood sugar levels caused by loss or defect of insulin-producing β-cells in the Islets of Langerhans. Type 1 diabetes (T1D) is caused by auto-imm... Diabetes mellitus is a chronic disease that impacts the homeostasis of blood sugar levels caused by loss or defect of insulin-producing β-cells in the Islets of Langerhans. Type 1 diabetes (T1D) is caused by auto-immune mediated destruction of β-cells, whereas in T2D, insulin is produced but used inefficiently. T2D accounts for 90% of people with diabetes worldwide (WHO 1999) and is the fastest increasing disease worldwide (http://gffzz89ee57209f824106sbcu6cb50wqpn6un5.ffgz.tsg.suse.edu.cn/en/). For an improved understanding of the pathomechanism of diabetes, profound knowledge of pancreas organogenesis and the associated gene regulatory networks is required. Therefore, we dissected and profiled the pancreatic endodermal and non-endodermal compartment between the embryonic stages (E) 12.5 and E 15.5 when progenitor cells commit to their different pancreatic lineages. Our associated study mined the global mRNA expression profile to increase the understanding of the secondary transition, endodermal-non-endodermal tissue interaction, and diabetic-related gene regulation. Furthermore, we validated 635 regulated pancreatic genes using the publicly available GenePaint.org, respective gp3.mpg.de to evaluate genes associated with genetic variants in Single-nucleotide polymorphism (SNP) related to T2D. 展开更多
关键词 Gene Expression Profile Pancreas Organogenesis Single-Nucleotide Polymorphism Type 1 Diabetes Type 2 Diabetes
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Expression profiling of primary and metastatic oral squamous cell carcinoma identifies progression-associated transcriptome changes and therapeutic vulnerabilities 认领 引用
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作者 Jonas Pyko Markus Glaβ +7 位作者 Julia Rosemann Matthias Kappler Jana Macho Sarah Qasem Stefan Hüttelmaier AlexanderWEckert Monika Haemmerle Tony Gutschner 《Cancer Communications》 SCIE CSCD 2025年第4期433-437,共5页
Oral squamous cell carcinoma(OSCC),a major subgroup of head and neck squamous cell carcinoma(HNSCC),is an aggressive disease that preferentially spreads to cervical lymph nodes.Positive lymph node status is an importa... Oral squamous cell carcinoma(OSCC),a major subgroup of head and neck squamous cell carcinoma(HNSCC),is an aggressive disease that preferentially spreads to cervical lymph nodes.Positive lymph node status is an important predictor of survival in OSCC[1-3].Hence,a better understanding of the molecular mechanisms underlying oral cancer metastasis and the identification of therapeutic vulnerabilities are needed to prevent and treat metastatic disease. 展开更多
关键词 molecular mechanisms head neck squamous cell carcinoma hnscc progression associated transcriptome changes therapeutic vulnerabilities expression profiling oral squamous cell carcinoma identification therapeutic vulnerabilities oral squamous cell carcinoma oscc
Comparative analysis of cytochrome P450-like genes from Locusta migratoria manilensis: expression profiling and response to insecticide exposure 认领 引用 被引量：4
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作者 Yan-Qiong Guo Jian-Zhen Zhang +4 位作者 Mei-Ling Yang Liang-Zhen Yan Kun Yan Zhu Ya-Ping Guo En-Bo Ma 《Insect Science》 SCIE CAS CSCD 2012年第1期75-85,共11页
The cytochrome P450 monooxygenase （cytochrome P450） gene superfamily comprises many genes that may be involved in the biotransformations of pesticides and other xenobiotics. To date, very little is known about cytoc... The cytochrome P450 monooxygenase （cytochrome P450） gene superfamily comprises many genes that may be involved in the biotransformations of pesticides and other xenobiotics. To date, very little is known about cytochrome P450 genes in the oriental migratory locust, Locusta migratoria manilensis. In this study, we carried out a genomewide analysis ofcytochrome P450 genes of the locust to identify putative cytochrome P450 genes and characterize their expression responses to insecticide exposures. We identified 15 cytochrome P450-1ike genes from a locust expressed sequence tag database （LocustDB）. Reverse transcription polymerase chain reaction （RT-PCR） analysis showed that most cytochrome P450-1ike genes displayed different tissue and developmental stage expression patterns. However, most of them were predominantly expressed in the midgnt, gastric caeca, fatbodies, and/or hindgut. Biochemical analysis showed that cytochrome P450 was differentially affected by three different insecticides. Deltamethrin caused significant inductions in 12 h at LD30 （dose to kill 30% of the tested individuals） in the nymphs, whereas malathion and carbaryl did not have significant effect on cytochrome P450 enzyme activity. Further RT-PCR analysis Showed significant increases of transcriptions of several cytochrome P450 genes in deltamethrin-treated locusts. Thus, the increased cytochrome P450 enzyme activity is likely due to increased transcriptions of multiple cytochrome P450 genes in response to deltamethrin exposure. These results are expected to help us better understand the interactions between insecticides and major detoxification enzymes, and possible changes of the susceptibility to other insecticides in deltamethrin-treated insects at various molecular levels. 展开更多
关键词 cytochrome P450 monooxygenase deltamethrin gene expression profiling insecticide Locusta migratoria manilensis
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MP3RNA-seq:Massively parallel 3’end RNA sequencing for high-throughput gene expression profiling and genotyping 认领 引用 被引量：4
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作者 Jian Chen Xiangbo Zhang +4 位作者 Fei Yi Xiang Gao Weibin Song Haiming Zhao Jinsheng Lai 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2021年第7期1227-1239,共13页
Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression profiling.However,its application tolarge‐scale experiments remains limited by costand labor constraints.Here we describe am... Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression profiling.However,its application tolarge‐scale experiments remains limited by costand labor constraints.Here we describe amassively parallel 3′end RNA‐seq(MP3RNA‐seq)method that introduces unique samplebarcodes during reverse transcription to permitsample pooling immediately following this initialstep.MP3RNA‐seq allows for handling of hun-dreds of samples in a single experiment,at acost of about$6 per sample for libraryconstruction and sequencing.MP3RNA‐seq iseffective for not only high‐throughput geneexpression profiling,but also genotyping.Todemonstrate its utility,we applied MP3RNA‐seqto 477 double haploid lines of maize.We iden-tified 19,429 genes expressed in at least 50%ofthe lines and 35,836 high‐quality singlenucleotide polymorphisms for genotypinganalysis.Armed with these data,we performedexpression and agronomic trait quantitativetrait locus(QTL)mapping and identified 25,797expression QTLs for 15,335 genes and 21 QTLsfor plant height,ear height,and relative earheight.We conclude that MP3RNA‐seq is highlyreproducible,accurate,and sensitive forhigh‐throughput gene expression profiling andgenotyping,and should be generally applicableto most eukaryotic species. 展开更多
关键词 gene expression profiling genotyping maize MP3RNA‐seq quantitative trait loci
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A genome-wide survey of maize lipid-related genes:candidate genes mining,digital gene expression profiling and colocation with QTL for maize kernel oil 认领 引用 被引量：2
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作者 LI Lin LI Hui +4 位作者 LI JiYing XU ShuTu YANG XiaoHong LI JianSheng YAN JianBing 《Science China(Life Sciences)》 SCIE CAS 2010年第6期690-700,共11页
Lipids play an important role in plants due to their abundance and their extensive participation in many metabolic processes.Genes involved in lipid metabolism have been extensively studied in Arabidopsis and other pl... Lipids play an important role in plants due to their abundance and their extensive participation in many metabolic processes.Genes involved in lipid metabolism have been extensively studied in Arabidopsis and other plant species.In this study,a total of 1003 maize lipid-related genes were cloned and annotated,including 42 genes with experimental validation,732 genes with full-length cDNA and protein sequences in public databases and 229 newly cloned genes.Ninety-seven maize lipid-related genes with tissue-preferential expression were discovered by in silico gene expression profiling based on 1984483 maize Expressed Sequence Tags collected from 182 cDNA libraries.Meanwhile,70 QTL clusters for maize kernel oil were identified,covering 34.5%of the maize genome.Fifty-nine(84%)QTL clusters co-located with at least one lipid-related gene,and the total number of these genes amounted to 147.Interestingly,thirteen genes with kernel-preferential expression profiles fell within QTL clusters for maize kernel oil content.All the maize lipid-related genes identified here may provide good targets for maize kernel oil QTL cloning and thus help us to better understand the molecular mechanism of maize kernel oil accumulation. 展开更多
关键词 lipid metabolism in silico gene cloning in silico gene expression profiling quantative trait locus(QTL) maize
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