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Identification of four differentially expressed genes associated with acute and chronic spinal cord injury based on bioinformatics data 被引量:1
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作者 Su-Ping Niu Ya-Jun Zhang +3 位作者 Na Han Xiao-Feng Yin Dian-Ying Zhang Yu-Hui Kou 《Neural Regeneration Research》 SCIE CAS CSCD 2021年第5期865-870,共6页
Complex pathological changes occur during the development of spinal cord injury(SCI),and determining the underlying molecular events that occur during SCI is necessary for the development of promising molecular target... Complex pathological changes occur during the development of spinal cord injury(SCI),and determining the underlying molecular events that occur during SCI is necessary for the development of promising molecular targets and therapeutic strategies.This study was designed to explore differentially expressed genes(DEGs)associated with the acute and chronic stages of SCI using bioinformatics analysis.Gene expression profiles(GSE45006,GSE93249,and GSE45550)were downloaded from the Gene Expression Omnibus database.SCI-associated DEGs from rat samples were identified,and Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed.In addition,a protein-protein interaction network was constructed.Approximately 66 DEGs were identified in GSE45550 between 3–14 days after SCI,whereas 2418 DEGs were identified in GSE450061–56 days after SCI.Moreover,1263,195,and 75 overlapping DEGs were identified between these two expression profiles,3,7/8,and 14 days after SCI,respectively.Additionally,16 overlapping DEGs were obtained in GSE450061–14 days after SCI,including Pank1,Hn1,Tmem150c,Rgd1309676,Lpl,Mdh1,Nnt,Loc100912219,Large1,Baiap2,Slc24a2,Fundc2,Mrps14,Slc16a7,Obfc1,and Alpk3.Importantly,3882 overlapping DEGs were identified in GSE932491–6 months after SCI,including 3316 protein-coding genes and 567 long non-coding RNA genes.A comparative analysis between GSE93249 and GSE45006 resulted in the enrichment of 1135 overlapping DEGs.The significant functions of these 1135 genes were correlated with the response to the immune effector process,the innate immune response,and cytokine production.Moreover,the biological processes and KEGG pathways of the overlapping DEGs were significantly enriched in immune system-related pathways,osteoclast differentiation,the nuclear factor-κB signaling pathway,and the chemokine signaling pathway.Finally,an analysis of the overlapping DEGs associated with both acute and chronic SCI,assessed using the expression profiles GSE93249 and GSE45006,identified four overlapping DEGs:Slc16a7,Alpk3,Lpl and Nnt.These findings may be useful for revealing the biological processes associated with SCI and the development of targeted intervention strategies. 展开更多
关键词 BIOINFORMATICS differential expression factor gene immune response INJURY PATHWAYS protein spinal cord
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LncRNA MEG8通过靶向miR-15a-5p调控MICA/B介导结直肠癌细胞免疫逃逸
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作者 李鸷 吴迪 +2 位作者 田飞 刘洁 谢兴明 《中国免疫学杂志》 CAS CSCD 北大核心 2024年第6期1217-1221,1127,共6页
目的:探究长链非编码RNA母系表达基因8(LncRNA MEG8)通过靶向miR-15a-5p调控MHCⅠ类相关蛋白A/B(MICA/B)介导的结直肠癌(CRC)细胞免疫逃逸机制。方法:RT-qPCR、Western blot检测CRC组织和细胞系MEG8、miR-15a-5p、MICA、MICB、NKG2D蛋... 目的:探究长链非编码RNA母系表达基因8(LncRNA MEG8)通过靶向miR-15a-5p调控MHCⅠ类相关蛋白A/B(MICA/B)介导的结直肠癌(CRC)细胞免疫逃逸机制。方法:RT-qPCR、Western blot检测CRC组织和细胞系MEG8、miR-15a-5p、MICA、MICB、NKG2D蛋白水平;双荧光素酶实验验证MEG8对miR-15a-5p的调控关系;采用脂质体转染法将NC、MEG8、miR-NC、miR-15a-5p分别或共转染至SW480、SW620细胞,记为NC组、MEG8组、MEG8+miR-NC组、MEG8+miR-15a-5p组;将NK细胞分别与SW480、SW620细胞共培养;ELISA检测共培养液中TNF-α、IFN-γ水平;CCK-8、EdU染色、Transwell实验检测细胞增殖、迁移和侵袭能力;RT-qPCR、Western blot检测细胞MEG8、miR-15a-5p、MICA、MICB、NKG2D蛋白水平。结果:与癌旁组织或正常结肠上皮细胞相比,CRC组织和细胞系中MEG8、MICA、MICB、NKG2D mRNA和蛋白水平降低,miR-15a-5p水平升高(P<0.05)。MEG8靶向调控miR-15a-5p。共培养体系中,与NC组相比,MEG8组细胞MICA、MICB、NKG2D蛋白水平、共培养上清液中TNF-α、IFN-γ水平明显升高,培养1 d、2 d、3 d后,OD值、EdU阳性率、迁移和侵袭细胞数明显降低(P<0.05);过表达miR-15a-5p能部分逆转过表达MEG8对细胞MICA、MICB、NKG2D、TNF-α、IFN-γ水平和增殖、侵袭转移能力的影响(P<0.05)。结论:MEG8通过靶向miR-15a-5p调控MICA、MICB表达,促进NK细胞活性,抑制CRC细胞免疫逃逸。 展开更多
关键词 长链非编码RNA母系表达基因8 miR-15a-5p 结直肠癌 免疫逃逸 MHCⅠ类相关蛋白A/B
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骨形态发生蛋白/Wnt信号通路调控成骨:揭示骨骼形成和重塑的分子机制 被引量:1
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作者 刘淏文 乔卫平 +3 位作者 孟志成 李凯杰 韩暄 史鹏博 《中国组织工程研究》 CAS 北大核心 2025年第3期563-571,共9页
背景:成骨细胞是负责骨骼形成和重塑的主要细胞类型,其功能的正常发挥受到多种信号通路的精密调控,其中,骨形态发生蛋白和Wnt信号通路在成骨过程中起着关键作用。目的:综述了骨形态发生蛋白/Wnt信号通路在调控成骨细胞功能中的作用,并... 背景:成骨细胞是负责骨骼形成和重塑的主要细胞类型,其功能的正常发挥受到多种信号通路的精密调控,其中,骨形态发生蛋白和Wnt信号通路在成骨过程中起着关键作用。目的:综述了骨形态发生蛋白/Wnt信号通路在调控成骨细胞功能中的作用,并分析其在不同生理和病理条件下的变化,以期进一步揭示骨骼形成和重塑的分子机制。方法:以中文检索词“BMP信号通路,Wnt信号通路,成骨”及英文检索词“BMP signaling pathway,Wnt signaling pathway,osteogenesis”在中国知网、万方和PubMed数据库中检索研究原著,检索时限为各数据库建库至2023年6月的相关文献,最终筛选61篇文献进行分析总结。采用文献综述的方法,对骨形态发生蛋白/Wnt信号通路调控成骨作用的研究进行梳理和分析。结果与结论:①骨形态发生蛋白和Wnt信号通路在成骨细胞的分化、增殖和成熟过程中发挥重要作用。骨形态发生蛋白信号通路主要通过激活Smad蛋白来调控成骨相关基因的表达,Smad蛋白被激活后进入细胞核,调控与成骨相关的基因表达,与骨形态发生蛋白不同,Wnt信号通路主要依赖于β-catenin的激活来发挥生物学效应。②不同生理和病理状态下,骨形态发生蛋白/Wnt信号通路的调控作用会受到多种因素的影响。生长因子及激素及机械应力等会在一定程度上影响骨形态发生蛋白/Wnt信号通路的活性。③骨形态发生蛋白/Wnt信号通路在调控成骨过程中与其他信号通路相互作用,共同构成复杂的调控网络。④中药和天然化合物可以通过调控信号通路来促进骨骼健康,为中药治疗骨骼疾病提供了新的可能性。⑤未来研究可进一步探讨骨形态发生蛋白/Wnt信号通路与其他信号通路的相互作用以及其在不同生理和病理条件下的变化,解析此复杂网络中的关键节点和调控机制,为骨骼相关疾病的治疗提供更精确的靶点,也为揭示骨骼形成和重塑的分子机制提供新的思路。 展开更多
关键词 骨形态发生蛋白信号通路 Wnt信号通路 成骨 骨骼 基因表达 分化 增殖 调控作用 交互作用 调控网络
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转录组测序分析外源水杨酸诱导茶树热激蛋白基因的响应
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作者 刘悦 曲浩 +3 位作者 田易萍 陈春林 冉隆珣 陈林波 《江苏农业学报》 CSCD 北大核心 2024年第4期607-614,共8页
水杨酸是诱导植物抗性机制中重要的信号分子,外源喷施水杨酸能够调控多种防御相关蛋白质,提升农作物的抗病能力。开展外源水杨酸诱导茶树抗性机制的研究能够挖掘抗病基因,为茶树抗病育种提供分子基础。本研究采集外源喷施水杨酸0 h、6 h... 水杨酸是诱导植物抗性机制中重要的信号分子,外源喷施水杨酸能够调控多种防御相关蛋白质,提升农作物的抗病能力。开展外源水杨酸诱导茶树抗性机制的研究能够挖掘抗病基因,为茶树抗病育种提供分子基础。本研究采集外源喷施水杨酸0 h、6 h、12 h、24 h、48 h的茶树叶片进行转录组测序与分析,结果表明,外源喷施水杨酸6 h、12 h、24 h、48 h时茶树叶片内差异表达基因数量分别为9 360个、3 399个、596个、115个,外源水杨酸处理后各时间点均发生差异表达的基因共604个。KEGG功能富集结果显示,处理后6 h时富集于植物激素信号转导、植物-病原菌互作、核糖体、剪接体和碳代谢通路上的差异表达基因数量分别为95个、73个、121个、94个、154个。差异表达基因中有12个热激因子基因、40个热激蛋白基因和12个WRKY家族转录因子基因上调表达。处理48 h后,无上调表达的热激因子基因,但仍有28个热激蛋白基因上调表达。病程相关蛋白基因在检测阶段均上调表达。外源水杨酸的诱导作用在处理6 h时最为明显,并且引起了大量热激蛋白的响应。本研究结果为开展外源水杨酸诱导茶树抗病机制和茶树抗病分子育种研究提供了参考。 展开更多
关键词 外源水杨酸 茶树 转录组 差异表达基因 热激蛋白
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静脉注射利多卡因后差异蛋白质的蛋白质组学分析
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作者 李翔 张永海 +6 位作者 杨凡 张玉 杨万吉 高冉 文岳 马少玲 马汉祥 《宁夏医科大学学报》 2024年第6期571-576,共6页
目的利用蛋白质组学技术定量分析静脉注射利多卡因(IVL)前后血清中差异蛋白质的表达。方法选取健康志愿者5例,IVL 1.5 mg·kg^(-1)后再以3 mg·(kg·h)^(-1)持续泵注30 min。IVL前和IVL后1 h各采集静脉血5 mL,通过串联质谱... 目的利用蛋白质组学技术定量分析静脉注射利多卡因(IVL)前后血清中差异蛋白质的表达。方法选取健康志愿者5例,IVL 1.5 mg·kg^(-1)后再以3 mg·(kg·h)^(-1)持续泵注30 min。IVL前和IVL后1 h各采集静脉血5 mL,通过串联质谱标记及高效液相色谱分离技术鉴定IVL后差异表达蛋白,并采用京都基因和基因组百科全书(KEGG)和基因本体论(GO)数据库分析鉴定差异蛋白的生物学信息。结果检测到IVL前后的血清中差异蛋白共15种,其中上调蛋白6种、下调蛋白9种。GO分析发现,大部分差异蛋白参与了细胞进程;亚细胞结构定位发现多数差异蛋白定位于细胞外区域及细胞质;功能富集分析发现多数蛋白参与炎性反应调节、B细胞的活化调控和蛋白质加工。上调蛋白组KEGG通路富集到p53信号通路。通过对上调组和下调组差异蛋白分析,发现差异蛋白依托泊苷诱导的2.4号蛋白(EI24)参与p53信号通路且调控钙离子浓度。结论IVL可能通过调控依托泊苷诱导的EI24和上池蛋白(SBSN)抑制肿瘤细胞的发生与发展;EI24可能通过调控细胞内钙离子浓度参与IVL产生的镇静作用。 展开更多
关键词 差异蛋白 基因本体论 富集分析 串联质谱标签 利多卡因
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幽门螺杆菌东亚型菌株GZ7/cagA^(+)和GZ7/ΔcagA源外膜囊泡的蛋白组学比较
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作者 彭国玲 周佳 +3 位作者 廖永慧 谢渊 周建奖 赵艳 《贵州医科大学学报》 CAS 2024年第5期636-644,共9页
目的通过分离、鉴定和比较细胞毒素相关基因A蛋白(cagA)、阳性幽门螺杆菌(H.pylori)、东亚型菌株GZ7/cagA^(+)及其cagA敲除菌株GZ7/ΔcagA来源的外膜囊泡(OMVs)中的差异表达蛋白(DEPs),分析cagA基因对OMVs中蛋白表达的影响。方法采用超... 目的通过分离、鉴定和比较细胞毒素相关基因A蛋白(cagA)、阳性幽门螺杆菌(H.pylori)、东亚型菌株GZ7/cagA^(+)及其cagA敲除菌株GZ7/ΔcagA来源的外膜囊泡(OMVs)中的差异表达蛋白(DEPs),分析cagA基因对OMVs中蛋白表达的影响。方法采用超速离心法分别提取GZ7/ΔcagA和GZ7/cagA^(+)的OMVs,通过透射电镜和纳米颗粒追踪技术鉴定其形态和粒径,使用Western blot技术验证两组OMVs中cagA蛋白的表达,分析OMVs的蛋白质组学;对蛋白组学数据进行质控分析和主成分分析鉴定后,以上调蛋白倍数变化(FC)>2.0、下调蛋白FC<0.5,FDR≤0.05为筛选条件筛选DEPs,利用OmicsBean在线工具、Gene Ontology和KOBAS对DEPs进行生物信息学分析;采用免疫荧光鉴定OMVs细胞在细胞中的定位,实时无标记细胞分析仪检测细胞活性。结果通过电镜和粒径证实成功分离纯化了OMVs;蛋白质组分析发现,GZ7/cagA^(+)-OMVs组与GZ7/ΔcagA-OMVs组比较有79个DEPs,其中38个蛋白下调、41个蛋白上调;生物信息学分析显示,DEPs主要与丙酮酸代谢、丙酸代谢、糖酵解/糖异生及柠檬酸循环等代谢途径有关;免疫荧光和实时无标记细胞分析证实H.pylori来源的OMVs能进入细胞并定位在线粒体并抑制细胞增殖。结论cagA能影响H.pylori分泌的OMVs中蛋白质的成分,DEPs可能促进cagA^(+)H.pylori在胃黏膜上的定植及致病性。 展开更多
关键词 幽门螺杆菌 细胞毒素相关基因A蛋白 胃癌 蛋白组 差异表达蛋白 线粒体
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高龄女性卵子颗粒细胞转录组的数据分析
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作者 秦立峰 王加强 朱伶 《中国组织工程研究》 CAS 北大核心 2025年第19期4069-4075,共7页
背景:颗粒细胞的状态很大程度上影响卵母细胞的质量。随着高龄女性在辅助生殖中占比不断增多,为了能更好地评估卵母细胞的质量,此研究在转录水平对不同年龄段患者来源的颗粒细胞进行了检测。目的:探究低龄和高龄患者颗粒细胞mRNA及长链... 背景:颗粒细胞的状态很大程度上影响卵母细胞的质量。随着高龄女性在辅助生殖中占比不断增多,为了能更好地评估卵母细胞的质量,此研究在转录水平对不同年龄段患者来源的颗粒细胞进行了检测。目的:探究低龄和高龄患者颗粒细胞mRNA及长链非编码RNA表达变化。方法:在辅助生殖治疗周期中收集患者取卵时获得的废弃卵丘颗粒细胞,其中低龄组患者年龄为25-35周岁,高龄组患者年龄为38-45周岁。对低龄和高龄女性颗粒细胞进行RNA-seq分析,每组3个重复。结果与结论:①RNA-seq分析结果显示,样本平均测序量超过14 G,质控后的数据质量Q30超过93%,数据平均比对率为98.4%,表明数据质量较好;②主成分分析及相关性分析结果显示高龄组和低龄组样本间基因表达水平具有明显差异;③差异分析结果显示,相对于低龄组,高龄组颗粒细胞中共有410个差异表达的mRNA,其中上调基因167个,下调基因243个,GO分析结果显示下调基因主要富集到胞吐作用调节、激素代谢过程等,GSEA分析结果显示高龄组颗粒细胞中与分泌相关的通路表达下调;④相对于低龄组,高龄组共检测到662个差异表达的长链非编码RNA,这部分长链非编码RNA直接调控的蛋白质编码基因为1772个,其中与差异表达基因交集59个。结果表明:高龄组颗粒细胞中与分泌相关的基因及通路表达下调,从而影响卵母细胞质量,同时这些表达下调的基因受到长链非编码RNA调控,因此长链非编码RNA的表达可能与年龄有关。 展开更多
关键词 年龄 颗粒细胞 卵母细胞 全转录组 差异基因 长链非编码基因
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RPS6亚基肽段抑制S180肿瘤细胞的分子机制
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作者 蒲帝宏 叶姿妤 +4 位作者 周丽倩 刘欣岚 鲁艳 侯怡铃 丁祥 《生物学杂志》 CAS CSCD 北大核心 2024年第2期32-38,共7页
为探究核糖体蛋白RPS6亚基肽段对S180肿瘤细胞基因表达的影响及抑制肿瘤细胞的关键分子和信号通路,以S180荷瘤小鼠为模型,用RPS6亚基肽段处理S180荷瘤小鼠,对S180肿瘤细胞进行Illumina测序获得差异表达的基因,并对这些差异基因进行GO和K... 为探究核糖体蛋白RPS6亚基肽段对S180肿瘤细胞基因表达的影响及抑制肿瘤细胞的关键分子和信号通路,以S180荷瘤小鼠为模型,用RPS6亚基肽段处理S180荷瘤小鼠,对S180肿瘤细胞进行Illumina测序获得差异表达的基因,并对这些差异基因进行GO和KEGG分析。基因表达结果显示,RPS6亚基肽段会导致mt-Cytb、mt-Nd1、Rpl13基因表达降低,阻碍S180肿瘤细胞的氧化磷酸化过程。GO分析结果显示,RPS6亚基肽段抑制肿瘤细胞关键门类集中于质膜和质膜外侧组成成分的变化及免疫反应调节和免疫细胞的激活。差异基因结果显示,RPS6亚基肽段通过增强PRL/PRLR信号,上调Uchl1基因表达,诱导肿瘤细胞周期停滞。KEGG通路富集分析结果显示,穿孔素(PRF1)和颗粒酶B(GZMB)表达诱导细胞凋亡,同时自然杀伤细胞(natural killer cell,NK)介导的细胞毒性与NF-κB信号通路信号增强,IFN-γ和TNF-α表达上调共同参与RPS6亚基肽段作用下的S180肿瘤细胞凋亡,抑制S180肿瘤细胞增殖。RPS6亚基肽段导致S180肿瘤细胞细胞周期停滞,并诱导自然杀伤细胞介导的细胞毒性及NF-κB信号通路的上调导致S180肿瘤细胞凋亡,为RPS6亚基肽段在抗肿瘤研究的应用提供一定的理论依据。 展开更多
关键词 核糖体蛋白RPS6 小分子多肽 RNA-Seq测序 差异表达基因 NF-κB信号通路
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蛋鸡脂肪肝出血综合征对肝脏及腹脂转录组的影响研究
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作者 易昕睿 马金虎 +7 位作者 王毅 王玉洁 朱枚子 李鑫宇 唐云书 薛敏 黄建珍 朱亚玲 《畜牧与兽医》 CAS 北大核心 2024年第2期37-45,共9页
旨在鉴定并比较脂肪肝出血综合征(FLHS)蛋鸡肝脏及腹脂组织的转录组特征,揭示FLHS发生发展中肝脏和腹脂调控的关键基因及潜在分子机制,为精确靶向肝脏及腹脂用药提供理论依据。采用高能低蛋白日粮构建蛋鸡FLHS模型,利用转录组测序(RNA-S... 旨在鉴定并比较脂肪肝出血综合征(FLHS)蛋鸡肝脏及腹脂组织的转录组特征,揭示FLHS发生发展中肝脏和腹脂调控的关键基因及潜在分子机制,为精确靶向肝脏及腹脂用药提供理论依据。采用高能低蛋白日粮构建蛋鸡FLHS模型,利用转录组测序(RNA-Seq)比较患鸡与正常组肝脏及腹脂基因表达图谱,利用基因本体(GO)功能注释、京都基因组百科全书(KEGG)通路富集和基因集富集分析(GSEA)阐明FLHS蛋鸡肝脏和腹脂差异基因的功能及作用通路;通过反转录PCR(RT-PCR)和RNA-Seq数据验证关键基因的差异表达。结果显示:高能低蛋白日粮可成功诱发蛋鸡FLHS,肝脏和腹脂转录谱发生明显改变。FLHS患鸡肝脏和腹脂中分别有443个(151上调表达,292下调表达)和526个(409上调表达,117下调表达)显著差异表达基因(|log2FC|≥1,P<0.05)。富集分析提示,包括磷酸烯醇丙酮酸羧激酶(PCK1)、载脂蛋白a-1(APOA1)在内的肝脏差异基因显著富集于代谢过程和PPAR信号通路而诱发肝脏脂质沉积;白细胞介素6(IL-6)、细胞因子信号通路抑制因子3(SOCS3)等腹脂差异基因更倾向于参与调控免疫过程和JAK-STAT信号通路导致炎症发生。提示:肝脏和腹脂通过不同途径共同参与蛋鸡FLHS发生发展,特异性靶向干扰肝脏及腹脂间关键差异基因及信号通路,对于优化FLHS的预防及治疗具有重要意义。 展开更多
关键词 高能低蛋白日粮 蛋鸡 脂肪肝出血综合征 转录组测序 差异基因
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急性髓系白血病患者血清lncRNA DANCR、lncRNA SNHG7表达及与病理特征、预后的关系
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作者 邹安琪 王悦 《标记免疫分析与临床》 CAS 2024年第2期253-258,共6页
目的探究急性髓系白血病(AML)患者血清长链非编码RNA抗分化非编码RNA(lncRNA DANCR)、长链非编码RNA小核仁RNA宿主基因7(lncRNA SNHG7)表达及与病理特征、预后的关系。方法选取2017年10月至2018年10月期间在本院就诊后出院的120例AML患... 目的探究急性髓系白血病(AML)患者血清长链非编码RNA抗分化非编码RNA(lncRNA DANCR)、长链非编码RNA小核仁RNA宿主基因7(lncRNA SNHG7)表达及与病理特征、预后的关系。方法选取2017年10月至2018年10月期间在本院就诊后出院的120例AML患者记为AML组,另选取120例在本院体检的志愿者记为对照组。观察并记录所有参与者年龄、性别、AML形态学分型等临床指标。实时荧光定量PCR(qRT-PCR)方法检测lncRNA DANCR、lncRNA SNHG7表达量;t检验方法分析lncRNA DANCR、lncRNA SNHG7表达差异及其与病理特征的关系;Pearson相关性分析二者表达水平的相关性;根据二者表达水平均值将AML患者分为lncRNA DANCR高表达组(n=65)和lncRNA DANCR低表达组(n=55)及lncRNA SNHG7高表达组(n=74)和lncRNA SNHG7低表达组(n=46);Kaplan-Meier法进行生存分析。结果AML患者lncRNA DANCR、lncRNA SNHG7水平显著高于对照组(P<0.05),且二者具有正相关性(r=0.414,P<0.001);LncRNA DANCR、lncRNA SNHG7表达水平与危险度分层、白细胞(WBC)、血红蛋白(Hb)及血小板计数(PLT)相关(P<0.05);高表达lncRNA DANCR、lncRNA SNHG7的AML患者5年生存率分别为30.77%、31.08%,低表达lncRNA DANCR、lncRNA SNHG7的AML患者5年生存率分别为50.91%、54.35%(P<0.05),低表达lncRNA DANCR、lncRNA SNHG7的AML患者生存率显著更高(P<0.05)。结论LncRNA DANCR、lncRNA SNHG7在AML患者血清中表达水平较高,两者具有的正相关性,可作为AML患者预后不良的重要指标。 展开更多
关键词 急性髓系白血病 长链非编码RNA抗分化非编码RNA 长链非编码RNA小核仁RNA宿主基因7 病理特征 预后
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基于临床生物信息学的白藜芦醇对自闭症谱系障碍的潜在治疗意义
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作者 吕艳华 钟小云 +2 位作者 王康龙 赵宏霞 于琦 《护理研究》 北大核心 2024年第21期3768-3778,共11页
目的:基于临床生物信息学探讨白藜芦醇对自闭症谱系障碍(ASD)的潜在治疗作用。方法:从基因表达综合数据库(GEO)中获取白藜芦醇和ASD的全基因组表达谱数据;分别对白藜芦醇和ASD的全基因组表达谱数据进行差异基因分析、基因本体(GO)富集... 目的:基于临床生物信息学探讨白藜芦醇对自闭症谱系障碍(ASD)的潜在治疗作用。方法:从基因表达综合数据库(GEO)中获取白藜芦醇和ASD的全基因组表达谱数据;分别对白藜芦醇和ASD的全基因组表达谱数据进行差异基因分析、基因本体(GO)富集分析、京都基因与基因组百科全书(KEGG)通路富集分析和蛋白质相互作用网络(PPI)分析并筛选核心基因;采用领域知识得分法在中英文数据库中对白藜芦醇具有重要调控作用核心基因的有效性进行文本验证。结果:白藜芦醇组和ASD组分别筛选出294个和256个差异基因(DEGs);白藜芦醇组GO富集的基因主要与神经系统发育、神经发生、突触组织等有关,KEGG通路富集主要与动物线粒体自噬、胆固醇代谢、甲状腺激素合成等有关;ASD组KEGG通路富集主要与丝裂原活化蛋白激酶信号通路、甲状腺激素合成、缩宫素信号通路等有关;白藜芦醇组DEGs的PPI网络分析中共获得11个核心基因,主要与细胞周期、突触发生和突触可塑性、炎症、免疫反应等有关。结论:白藜芦醇具有抑制炎症反应、促进免疫调节、改善氧化应激、调节突触发生和突触生成过程、调节神经递质的释放等功能,对ASD具有潜在的治疗意义。 展开更多
关键词 白藜芦醇 自闭症谱系障碍 差异基因分析 富集分析 蛋白质相互作用网络 领域知识得分 临床生物信息学
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左心室辅助装置对心肌病心肌转录组影响
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作者 张纯溪 王钊 《生物医学工程与临床》 CAS 2024年第5期709-716,共8页
目的探讨左心室辅助装置(LVAD)对终末期心肌病患者心肌基因表达谱改变及其生物学意义。方法从GEO数据库(http://www.ncbi.nlm.nih.gov/geo)检索并筛选植入LVAD的终末期射血分数降低型心力衰竭患者心肌mRNA表达谱数据集。用韦恩图分析工... 目的探讨左心室辅助装置(LVAD)对终末期心肌病患者心肌基因表达谱改变及其生物学意义。方法从GEO数据库(http://www.ncbi.nlm.nih.gov/geo)检索并筛选植入LVAD的终末期射血分数降低型心力衰竭患者心肌mRNA表达谱数据集。用韦恩图分析工具筛选目标数据集的共有差异表达基因(DEG)。选择来自至少2个数据集的DEG进入后续分析。用GEO2R筛选DEG,用GSE52601验证DEG。对DEG进行基因本体论(GO)、京都基因与基因组百科全书(KEGG)和基因集富集分析(GSEA),用STRING和Cytoscape构建蛋白-蛋白互作网络,识别核心模块和枢纽基因。结果共检索出4个目标数据集GSE430、GSE974、GSE21610、GSE52601。前3个作为训练集;GSE52601为验证集,对筛选出的核心DEG进行验证。共鉴定33个DEG(22个下调、11个上调),与中性粒细胞脱颗粒和G蛋白偶连受体配体结合相关;筛选出一个由15个枢纽基因组成的核心模块,与对炎症损伤的响应及调控、趋化因子经G蛋白偶联受体介导的信号转导相关,涉及丝裂原活化蛋白(MAP)/细胞外信号调节激酶(ERK)、肌动蛋白丝、γ-氨基丁酸β(GABA-B)受体、唾液酸、前列蛋白E受体、CD40受体和白细胞介素8受体等通路,尿激酶型纤溶酶原激活剂基因(PLAU)和CD163分子基因(CD163)在验证集中呈现相同变化趋势。结论LVAD对心肌病理重构的分子机制与趋化因子经G蛋白偶联受体介导的炎症通路相关,为选择合适的LVAD类型和评估LVAD治疗效果提供了基因水平的依据。 展开更多
关键词 左心室辅助装置 机械辅助循环 心力衰竭 生物信息学分析 转录组 差异表达基因 蛋白-蛋白互作网络
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长链非编码RNA母系表达基因8通过微小RNA-495-3p调控急性髓性白血病细胞高迁移率族蛋白A1表达及对细胞增殖、凋亡的作用机制研究
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作者 张璐 郭含梦 王庆义 《陕西医学杂志》 CAS 2024年第7期895-899,共5页
目的:探讨长链非编码RNA(lncRNA)母系表达基因8(MEG8)通过微小RNA-495-3p(miR-495-3p)调控急性髓性白血病细胞(AML)高迁移率族蛋白A1(HMGA1)表达及对细胞增殖、凋亡的机制。方法:选取50例经确诊为AML患者的骨髓活检标本与52例健康骨髓... 目的:探讨长链非编码RNA(lncRNA)母系表达基因8(MEG8)通过微小RNA-495-3p(miR-495-3p)调控急性髓性白血病细胞(AML)高迁移率族蛋白A1(HMGA1)表达及对细胞增殖、凋亡的机制。方法:选取50例经确诊为AML患者的骨髓活检标本与52例健康骨髓捐赠者骨髓标本,常规培养人AML细胞株HL-60,采用实时荧光定量PCR(RT-qPCR)法骨髓单个核细胞中lncRNA MEG8 mRNA表达。将HL-60细胞分为六组,即HL-60组(HL-60细胞)、si-NC组(转染si-NC)、si-lncRNA MEG8组(转染si-lncRNA MEG8)、mimic-NC组(转染mimic-NC)、miR-495-3p mimic组(转染miR-495-3p mimic)、si-lncRNA MEG8+miR-495-3p mimic组(转染si-lncRNA MEG8+miR-495-3p mimic),CCK-8法检测培养24、48、72 h各组细胞增殖能力,流式细胞术检测细胞凋亡,Western blot法检测细胞中HMGA1表达,双荧光素酶报告基因实验验证lncRNA MEG8、miR-495-3p、HMGA1之间的关系。结果:与对照组相比,观察组lncRNA MEG8 mRNA表达升高(P<0.05)。与miR NC+MEG8 WT组比较,miR-495-3p mimic+MEG8 WT组荧光素酶活性下降(P<0.05),与miR NC+HMGA1 WT组比较,miR-495-3p mimic+HMGA1 WT组荧光素酶活性下降(P<0.05)。与HL-60组、si-NC组、mimic-NC组比较,si-lncRNA MEG8组、miR-495-3p mimic组和si-lncRNA MEG8+miR-495-3p mimic组24、48 h细胞增殖能力均显著下降,si-lncRNA MEG8+miR-495-3p mimic组细胞增殖率最低(P<0.05)。与HL-60组、si-NC组和mimic-NC组比较,si-lncRNA MEG8+miR-495-3p mimic组HL-60细胞凋亡率高于si-lncRNA MEG8组和miR-495-3p mimic组(均P<0.05)。与HL-60组、si-NC组和mimic-NC组比较,si-lncRNA MEG8+miR-495-3p mimic组HMGA1蛋白表达低于si-lncRNA MEG8组和miR-495-3p mimic组(均P<0.05)。结论:沉默lncRNA MEG8可能通过上调miR-495-3p来下调HMGB1,来抑制HL-60细胞的恶性生物学行为,可为探索AML潜在治疗靶点提供了新思路。 展开更多
关键词 长链非编码RNA 母系表达基因8 微小RNA-495-3p 急性髓性白血病细胞 高迁移率族蛋白1
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SPP1、DEC1、C1QTNF6蛋白与口腔鳞状细胞癌患者临床病理指标及预后的关系
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作者 付勇青 徐三会 +1 位作者 赵岩 王丽丽 《癌变.畸变.突变》 CAS 2024年第2期107-111,117,共6页
目的:探讨口腔鳞状细胞癌患者血清重组人分泌型磷蛋白1(SPP1)、软骨分化的表达基因1(DEC1)和补体C1q/肿瘤坏死因子相关蛋白6(C1QTNF6)的表达水平与其临床病理指标及预后的关系。方法:免疫组织化学染色法和电化学发光免疫分析法检测88例... 目的:探讨口腔鳞状细胞癌患者血清重组人分泌型磷蛋白1(SPP1)、软骨分化的表达基因1(DEC1)和补体C1q/肿瘤坏死因子相关蛋白6(C1QTNF6)的表达水平与其临床病理指标及预后的关系。方法:免疫组织化学染色法和电化学发光免疫分析法检测88例口腔鳞状细胞癌患者癌组织和血清中SPP1、DEC1和C1QTNF6蛋白的表达水平;Pearson相关性分析和Kaplan-Meier生存分析法分析患者血清SPP1、DEC1和C1QTNF6蛋白表达水平与其临床病理指标的相关性和对患者预后的影响。多因素Cox回归法分析影响口腔鳞状细胞癌患者预后的危险因素。结果:免疫组织化学染色结果显示口腔鳞状细胞癌患者癌组织中SPP1、DEC1和C1QTNF6蛋白的阳性表达率较癌旁组织分别增加了1.94、2.98和2.35倍(P<0.05或P<0.01);电化学发光免疫分析法结果显示口腔鳞状细胞癌患者血清SPP1、DEC1和C1QTNF6蛋白表达水平较正常人分别上调了8.61、6.20和4.03倍(P<0.05或P<0.01);Pearson相关性分析结果显示患者血清SPP1、DEC1和C1QTNF6蛋白表达水平与患者发生多灶嗜神经侵犯、肿瘤浸润程度、淋巴结转移、较高的TNM分期呈正相关(P<0.05);Kaplan-Meier生存分析结果显示,血清SPP1、DEC1和C1QTNF6蛋白高表达水平的口腔鳞状细胞癌患者总生存率低;多因素Cox回归分析结果表明多灶嗜神经侵犯、肿瘤高浸润度、淋巴结转移和高的TNM分期是影响预后的危险因素(P<0.05)。结论:口腔鳞状细胞癌患者癌组织和血清中SPP1、DEC1和C1QTNF6蛋白表达水平升高,且与患者发生多灶嗜神经侵犯、肿瘤浸润和淋巴结转移、较高的TNM分期呈正相关,而与患者预后呈负相关。 展开更多
关键词 口腔鳞状细胞癌 重组人分泌型磷蛋白1 软骨分化的表达基因1 补体C1q/肿瘤坏死因子相关蛋白6 预后
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Bioinformatics analysis of microarray data to explore the key genes involved in HSF4 mutation-induced cataract 被引量:4
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作者 Rui Tian Yang Xu +1 位作者 Wen-Wen Dou Hui Zhang 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2018年第6期910-917,共8页
AIM: To reveal the mechanisms of heat-shock transcription factor 4 (HSF4) mutation-induced cataract.METHODS: GSE22362, including 3 HSF4-null lens and 3 wild-type lens, was obtained from Gene Expression Omnibus dat... AIM: To reveal the mechanisms of heat-shock transcription factor 4 (HSF4) mutation-induced cataract.METHODS: GSE22362, including 3 HSF4-null lens and 3 wild-type lens, was obtained from Gene Expression Omnibus database. After data preprocessing, the differentially expressed genes (DEGs) were identified using the limma package. Based on Database for Annotation, Visualization and Integrated Discovery (DAVID) tool, functional and pathway enrichment analyses were performed for the DEGs. Followed by protein-protein interaction (PPI) network was constructed using STRING database and Cytoscape software. Furthermore, the validated microRNA (miRNA)-DEG pairs were obtained from miRWalk2.0 database, and then miRNA-DEG regulatory network was visualized by Cytoscape software. RESULTS: A total of 176 DEGs were identified in HSF4-null lens compared with wild-type lens. In the PPI network, FBJ osteosarcoma oncogene (FOS), early growth response 1 (EGR1) and heme oxygenase (decycling) 1 (HMOX1) had higher degrees and could interact with each other. Besides, mmu-miR-15a-5p and mmu-miR-26a-5p were among the top 10 miRNAs in the miRNA-DEG regulatory network. Additionally, mmu-miR-26a-5p could target EGR1 in the regulatory network. CONCLUSION: FOS, EGR1, HMOX1, mmu-miR-26a-5p and mmu-miR-15a-5p might function in the pathogenesis of HSF4 mutation-induced cataract. 展开更多
关键词 CATARACT heat-shock transcription factor 4 differentially expressed genes protein-protein interaction network regulatory network
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Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish 被引量:2
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作者 Jia-He Li Zhong-Ju Shi +6 位作者 Yan Li Bin Pan Shi-Yang Yuan Lin-Lin Shi Yan Hao Fu-Jiang Cao Shi-Qing Feng 《Neural Regeneration Research》 SCIE CAS CSCD 2020年第1期103-111,共9页
Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord ... Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord injury,whereas humans cannot.To analyze differentially expressed zebrafish genes between axon-regenerated neurons and axon-non-regenerated neurons after spinal cord injury,and to explore the key genes and pathways of axonal regeneration after spinal cord injury,microarray GSE56842 was analyzed using the online tool,GEO2R,in the Gene Expression Omnibus database.Gene ontology and protein-protein interaction networks were used to analyze the identified differentially expressed genes.Finally,we screened for genes and pathways that may play a role in spinal cord injury repair in zebrafish and mammals.A total of 636 differentially expressed genes were obtained,including 255 up-regulated and 381 down-regulated differentially expressed genes in axon-regenerated neurons.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment results were also obtained.A protein-protein interaction network contained 480 node genes and 1976 node connections.We also obtained the 10 hub genes with the highest correlation and the two modules with the highest score.The results showed that spectrin may promote axonal regeneration after spinal cord injury in zebrafish.Transforming growth factor beta signaling may inhibit repair after spinal cord injury in zebrafish.Focal adhesion or tight junctions may play an important role in the migration and proliferation of some cells,such as Schwann cells or neural progenitor cells,after spinal cord injury in zebrafish.Bioinformatic analysis identified key candidate genes and pathways in axonal regeneration after spinal cord injury in zebrafish,providing targets for treatment of spinal cord injury in mammals. 展开更多
关键词 axonal REGENERATION differentially expressed genes focal ADHESIONS Gene Ontology Kyoto Encyclopedia of genes and Genomes neural REGENERATION protein-protein interaction network SIGNALING PATHWAY SPECTRIN tight junctions transforming growth factor beta Wnt SIGNALING PATHWAY
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A Rice CaMBP Gene is Induced in Organ-Specific Manner by Both Chilling and Heat-Shock Treatments
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作者 WAN Jia XI Jiang +1 位作者 Do Zhi-ru Xu Zheng-jun 《Rice science》 SCIE 2008年第3期166-172,共7页
A rice CaMBP gene, OsCaMBP (AB363406), was isolated from a chilling treated rice using the fluorescent differential display (FDD) screening method. Its cDNA sequence (2094 bp) contains an opening reading frame ... A rice CaMBP gene, OsCaMBP (AB363406), was isolated from a chilling treated rice using the fluorescent differential display (FDD) screening method. Its cDNA sequence (2094 bp) contains an opening reading frame (ORF) encoding a 569 amino acids protein (63.2 kD). OsCaMBP has the typical structural features of the CaMBP family, including the conserved IQ calmodulin-binding motif at the N-terminus. Homology analysis revealed 38.25%-47.28% identities of OsCaMBP with other CaMBPs in plants. RT-PCR analysis showed that the expression of OsCaMBP was remarkably inducible under the chilling (8℃) and heat-shock (42℃) treatments. OsCaMBP was undetectable under the normal conditions, and induced under the chilling treatment for 1 h, as well as the heat-shock treatment for 15 min, suggesting that the gene plays important roles in the signaling pathway in rice under both chilling and heat-shock stresses. 展开更多
关键词 rice (Oryza sativa) calmodulin-binding protein fluorescent differential display gene cloning organ-specific expression
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RNA-binding proteins related to stress response and differentiation in protozoa
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作者 Lysangela Ronalte Alves Samuel Goldenberg 《World Journal of Biological Chemistry》 CAS 2016年第1期78-87,共10页
RNA-binding proteins(RBPs) are key regulators of gene expression. There are several distinct families of RBPs and they are involved in the cellular response to environmental changes, cell differentiation and cell deat... RNA-binding proteins(RBPs) are key regulators of gene expression. There are several distinct families of RBPs and they are involved in the cellular response to environmental changes, cell differentiation and cell death. The RBPs can differentially combine with RNA molecules and form ribonucleoprotein(RNP) complexes, defining the function and fate of RNA molecules in the cell. RBPs display diverse domains that allow them to be categorized into distinct families. They play important roles in the cellular response to physiological stress, in cell differentiation, and, it is believed, in the cellular localization of certain mRNAs. In several protozoa, a physiological stress(nutritional, temperature or pH) triggers differentiation to a distinct developmental stage. Most of the RBPs characterized in protozoa arise from trypanosomatids. In these protozoa gene expression regulation is mostly post-transcriptional, which suggests that some RBPs might display regulatory functions distinct from those described for other eukaryotes. mRNA stability can be altered as a response to stress. Transcripts are sequestered to RNA granules that ultimately modulate their availability to the translation machinery, storage or degradation, depending on the associated proteins. These aggregates of mRNPs containing mRNAs that are not being translated colocalize in cytoplasmic foci, and their numbers and size vary according to cell conditions such as oxidative stress, nutritional status and treatment with drugs that inhibit translation. 展开更多
关键词 Gene expression regulation RNA-BINDING proteins RNA-protein COMPLEXES RNA GRANULES PROTOZOA Stress and cell differentiation
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Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis
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作者 YANG Yue MA Yu-ting +12 位作者 LIU Yang-yang Demar LYLE LI Dong-dong WANG Ping-xi XU Jia-liang ZHEN Si-han LU Jia-wen PENG Yun-ling CUI Yu FU Jun-jie DU Wan-li ZHANG Hong-wei WANG Jian-hua 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2022年第5期1266-1277,共12页
Deep-sowing is an important method for avoiding drought stress in crop species,including maize.Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing toler... Deep-sowing is an important method for avoiding drought stress in crop species,including maize.Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance.This study evaluated four traits(mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12)related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms(SNPs).The genomewide association study detected that 273 SNPs were in linkage disequilibrium(LD)with the genetic basis of maize deep-sowing tolerance.The RNA-sequencing analysis identified 1944 and 2098 differentially expressed genes(DEGs)in two comparisons,which shared 281 DEGs.By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs,we identified seven candidate genes,of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein.GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length,auxin,or light response.Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length.Gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines.These results suggest that GRMZM2G119769 is the most likely candidate gene.This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes,which would be useful for further research on maize deep-sowing tolerance. 展开更多
关键词 MAIZE mesocotyl length association mapping differentially expressed gene SNF1 kinase interactor-like protein
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Analysis of Proteotranscriptomics Landscape Reveals Differentially Regulated Pathways in Toxoplasma gondii Infected Mouse Liver
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作者 Tanzina Tarannum Md. Saruar Alam +3 位作者 Atiqur Rahman Sajib Chakraborty Hossain Uddin Shekhar Taibur Rahman 《Computational Molecular Bioscience》 2022年第1期20-57,共38页
Toxoplasma gondii (T. gondii) an intracellular protozoan parasite, infects mammals including human population world-wide. Upon primary infection, the parasite contributes to mild flu like symptoms in immune competent ... Toxoplasma gondii (T. gondii) an intracellular protozoan parasite, infects mammals including human population world-wide. Upon primary infection, the parasite contributes to mild flu like symptoms in immune competent host, but life threatening complication is seen in immune compromised patients and in pregnant women. Understanding the host-parasite interaction is critical for understanding the pathogenesis and biology parasite reactivation in the host. In this study, we used proteotrasncriptomics analyses by integrating the transcriptomics and proteomics data of T. gondii infected mouse liver to uncover the effector molecules responsible for disease pathogenesis that can be used as candidate markers for diagnosis and drug target. With this aim, we systematically integrated transcriptomicand proteomic data, representing the parasite infected mouse liver. Out of 2758 differentially expressed genes (DEGs) and 301 differentially expressed proteins (DEPs), 159 overlapping genes were identified. Among them, 86 genes were upregulated and 72 were downregulated in their respective mRNA and protein levels in the infected condition. Gene Ontology (GO) analysis revealed that the upregulated genes were mostly associated with immune system processes whereas the downregulated genes were involved in oxidation-reduction process and metabolism of lipid, and fatty acids. Protein-protein interaction (PPI) network analysis uncovered an interaction-hub including, Psmb8, Psmb9 and Tap1 for upregulated proteins and Cyp1A2, Cyp4A10 and Cyp3A11 for down-regulated proteins. Further studies are needed to validating these effector molecules. These molecules are likely to play a vital role in disease pathogenesis, as well as can be used as potential diagnostic marker and drug target candidates. 展开更多
关键词 Toxoplasma gondii Transcriptome PROTEOME Mouse Liver differentially expressed genes and proteins Gene Ontology Analysis Protein-Protein Interaction Hub-proteins Homology Modeling Effector Molecules
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