Systematic identification of human housekeeping genes possibly useful as references in gene expression studies.
Systematic identification of human housekeeping genes possibly useful as references in gene expression studies.
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DOI：
10.3892/mmr.2017.6944
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发表时间：
2017-09
影响因子：
3.4
通讯作者：
Pelleri MC
中科院分区：
文献类型：
--
作者：
Caracausi M;Piovesan A;Antonaros F;Strippoli P;Vitale L;Pelleri MC
用于研究特定生物体中基因表达的理想参考或对照基因应在中高水平表达以便于检测，应在不同类型的细胞中和在经历不同处理的同一细胞类型中以恒定/稳定的水平表达，并应在生物体的许多不同组织中保持这些特征。从生物学的角度来看，理想参考基因的这些理论要求似乎最适合管家(HK)基因。在人类表达微阵列数据的质量和完整性及其统计分析方面的最新进展可能为生物学和医学中的人类基因表达研究的量化标准化提供新的线索，包括组织内和跨组织。本研究使用的系统方法以Transcriptome Mapper工具为基础，利用自动将探针重新分配到相应基因、样本内和样本间归一化、在一个有索引和可搜索的数据库内以线性形式阐述和表示基因表达值的方法，该数据库具有一个图形界面，记录了31,000多个转录本的表达定量水平、表达可变性和跨组织表达宽度。本研究对54个不同组织的646个表达谱数据集进行了荟萃分析，确定肌动蛋白γ1是最符合所有传统标准组合的HK基因，可以作为通用参考基因；还鉴定了两个核糖体蛋白基因RPS18和RPS27，以及一个水通道基因POM121跨膜核孔素C。本研究提供了可能最适合下列单个组织/器官的特定组织和器官基因清单：脂肪组织、骨髓、脑、心脏、肾脏、肝脏、肺、卵巢、骨骼肌和睾丸；在这些情况下，本研究还以可搜索的数据库表格的形式提供了具有代表性的、量化的相对典型基因表达图谱。
The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium-high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross- and within-tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra- and inter-sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross-tissue width of expression for more than 31,000 transcripts. The present study conducted a meta-analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue- and organ-specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative, quantitative portrait of the relative, typical gene-expression profile in the form of searchable database tables.
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影响因子：
3.7
作者：
Ersahin T;Carkacioglu L;Can T;Konu O;Atalay V;Cetin-Atalay R
通讯作者：
Cetin-Atalay R
影响因子：
3.7
作者：
de Jonge HJ;Fehrmann RS;de Bont ES;Hofstra RM;Gerbens F;Kamps WA;de Vries EG;van der Zee AG;te Meerman GJ;ter Elst A
通讯作者：
ter Elst A
影响因子：
2.9
作者：
BHATIA, P;TAYLOR, WR;WRIGHT, JA
通讯作者：
WRIGHT, JA
影响因子：
5.8
作者：
Berriz, GF;King, OD;Roth, FP
通讯作者：
Roth, FP
影响因子：
5.6
作者：
Caracausi, Maria;Piovesan, Allison;Pelleri, Maria Chiara
通讯作者：
Pelleri, Maria Chiara