NCI60(made4)
NCI60()所属R语言包：made4
Microarray gene expression profiles of the NCI 60 cell lines
基因芯片的NCI 60单元株的基因表达谱
译者：生物统计家园网 机器人LoveR
描述----------Description----------
NCI60 is a dataset of gene expression profiles of 60 National Cancer Institute (NCI) cell lines. These 60 human tumour cell lines are derived from patients with leukaemia, melanoma, along with, lung, colon, central nervous system, ovarian, renal, breast and prostate cancers. This panel of cell lines have been subjected to several different DNA microarray studies using both Affymetrix and spotted cDNA array technology. This dataset contains subsets from one cDNA spotted (Ross et al., 2000) and one Affymetrix (Staunton et al., 2001) study, and are pre-processed as described by Culhane et al., 2003.
NCI60是60国立癌症研究所（NCI）的单元株的基因表达谱数据集。来自白血病，黑色素瘤患者，其中60人肿瘤单元株，肺癌，结肠癌，中枢神经系统，卵巢，肾，乳腺癌和前列腺癌。该单元系已受到几种不同的DNA芯片研究，同时使用Affymetrix公司和斑点cDNA阵列技术。该数据集包含一个cDNA斑点（Ross等人，2000年）和1 Affymetrix公司（士丹顿等人，2001年）的研究子集，是前处理Culhane等。，2003。
用法----------Usage----------
data(NCI60)
格式----------Format----------
The format is: List of 3
格式是：3
\$Ross:data.frame containing 144 rows and 60 columns. 144 gene expression log ratio measurements of the NCI60 cell lines.
\ $罗斯：data.frame包含144行和60列。 144个基因的表达log的NCI60单元株的比例测量。
\$Affy:data.frame containing 144 rows and 60 columns. 144 Affymetrix gene expression average difference measurements of the NCI60 cell lines.
\ $ Affy：data.frame包含144行和60列。 144 Affymetrix基因表达的平均差异测量的NCI60单元株。
\$classes ata matrix of 60 rows and 2 columns. The first column contains the names of the 60 cell line which were analysed. The second column lists the 9 phenotypes of the cell lines, which are BREAST, CNS, COLON, LEUK, MELAN, NSCLC, OVAR, PROSTATE, RENAL.
\ $类：数据matrix60行2列。第一列包含60单元系进行了分析的名字。第二列列出了9单元株的表型，这是乳腺癌，中枢神经系统，结肠癌，MELAN，略，非小单元肺癌，OVAR，前列腺癌，肾。
\$Annotata matrix of 144 rows and 4 columns. The 144 rows contain the 144 genes in the \$Ross and \$Affy datasets, together with their Unigene IDs, and HUGO Gene Symbols. The Gene Symbols obtained for the \$Ross and \$Affy datasets differed (see note below), hence both are given. The columns of the matrix are the IMAGE ID of the clones of the \$Ross dataset, the HUGO Gene Symbols of these IMAGE clone ID obtained from SOURCE, the Affymetrix ID of the \$Affy dataset, and the HUGO Gene Symbols of these Affymetrix IDs obtained using annaffy.
\ $ Annot：数据matrix144行和4列。 144行包含的144个基因在\ $罗斯和\ $ Affy集，连同他们Unigene的标识，和雨果的基因符号。 \ $罗斯和\ $ Affy集获得的基因符号不同（见下面的说明），因此都给予。列matrix形象的\ $罗斯集“的克隆ID，从这些图像克隆ID雨果基因符号源，Affymetrix公司的ID \ $ Affy集，和雨果基因Affymetrix公司的标识，这些符号获得使用annaffy。
Details
详情----------Details----------
The datasets were processed as described by Culhane et al., 2003.
被处理的数据集Culhane等所述，2003年。
The Ross data.frame contains gene expression profiles of each cell lines in the NCI-60 panel, which were determined using spotted cDNA arrays containing 9,703 human cDNAs (Ross et al., 2000). The data were downloaded from The NCI Genomics and Bioinformatics Group Datasets resource http://discover.nci.nih.gov/datasetsNature2000.jsp. The updated version of this dataset (updated 12/19/01) was retrieved. Data were provided as log ratio values.
罗斯data.frame包含的NCI-60面板，其中确定使用含9703人的cDNAs（Ross等人，2000年）发现的cDNA阵列中每个单元株的基因表达谱。来自国家癌症研究所基因组学和生物信息集团的数据集资源http://discover.nci.nih.gov/datasetsNature2000.jsp下载数据。被检索的数据集（01年12月19日更新）的更新版本。数据提供了作为log比值。
In this study, rows (genes) with greater than 15 and were removed from analysis, reducing the dataset to 5643 spot values per cell line. Remaining missing values were imputed using a K nearest neighbour method, with 16 neighbours and a Euclidean distance metric (Troyanskaya et al., 2001). The dataset \$Ross contains a subset of the 144 genes of the 1375 genes set described by Scherf et al., 2000. This datasets is available for download from http://bioinf.ucd.ie/people/aedin/R/.
在这项研究中，大于15和行（基因）被拆除，从分析，降低了每单元线5643点值的数据集。其余遗漏值归咎于使用的K近邻方法，与16个邻国和欧几里德距离度量（Troyanskaya等，2001）。 \ $罗斯的数据集包含144基因舍夫等人，2000年设定的1375基因的一个子集。这个数据集是可用可从http://bioinf.ucd.ie/people/aedin/R/下载。
In order to reduce the size of the example datasets, the Unigene ID's for each of the 1375 IMAGE ID's for these genes were obtained using SOURCE http://source.stanford.edu. These were compared with the Unigene ID's of the 1517 gene subset of the \$Affy dataset. 144 genes were common between the two datasets and these are contained in \$Ross.
为了减少，例如数据集的大小，Unigene的编号是1375图片编号每个这些基因，获得了使用源http://source.stanford.edu。这些Unigene的编号Affy集\ $ 1517的基因子集进行比较。 144个基因的两个数据集之间的共同，这些包含在\ $罗斯。
The Affy data were derived using high density Hu6800 Affymetrix microarrays containing 7129 probe sets (Staunton et al., 2001). The dataset was downloaded from the Whitehead Institute Cancer Genomics supplemental data to the paper from Staunton et al., http://www-genome.wi.mit.edu/mpr/NCI60/, where the data were provided as average difference (perfect match-mismatch) values. As described by Staunton et al., an expression value of 100 units was assigned to all average difference values less than 100. Genes whose expression was invariant across all 60 cell lines were not considered, reducing the dataset to 4515 probe sets. This dataset NCI60\$Affy of 1517 probe set, contains genes in which the minimum change in gene expression across all 60 cell lines was greater than 500 average difference units. Data were logged (base 2) and median centred. This datasets is available for download from http://bioinf.ucd.ie/people/aedin/R/.
Affy数据，推导出使用高的密度Hu6800 Affymetrix公司芯片包含7129探针台（士丹顿等人，2001年）。怀特黑德研究所的癌症基因组学的补充数据士丹顿等。http://www-genome.wi.mit.edu/mpr/NCI60/，从纸张数据集下载提供的数据为平均差异（完美匹配不匹配）值。士丹顿等人。，100个单位的表达式的值被分配到所有小于100的平均差值。基因的表达，在所有60单元系不变，不考虑，减少到4515个探针组的数据集。本集NCI60 \ $ Affy 1517年的探针组，包含基因在所有60个单元株基因表达的变化最小的是大于500的平均差异单位。数据被记录（碱基）和集中的中位数。这个数据集是可用可从http://bioinf.ucd.ie/people/aedin/R/下载。
In order to reduce the size of the example datasets, the Unigene ID's for each of the 1517 Affymetrix ID of these genes were obtained using the function aafUniGene in the annaffy Bioconductor package. These 1517 Unigene IDs were compared with the Unigene ID's of the 1375 gene subset of the \$Ross dataset. 144 genes were common between the two datasets and these are contained in \$Affy.
为了减少，例如数据集的大小，Unigene的编号是1517 Affymetrix公司对这些基因的ID分别获得使用功能aafUniGeneannaffyBioconductor包。 Unigene的编号1375基因子集的\ $罗斯集是这些1517 Unigene的标识进行比较。 144个基因的两个数据集之间的共同，这些包含在\ $ Affy。
源----------Source----------
These pre-processed datasets were available as a supplement to the paper:
这些前处理的数据集可作为纸张的补充：
Culhane AC, Perriere G, Higgins DG. Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics. 2003 Nov 21;4(1):59. http://www.biomedcentral.com/1471-2105/4/59
culhane交流，Perriere G，希金斯总干事。跨平台使用共同的惯性分析基因表达数据的比较和可视化。 BMC的生物信息学。 2003年11月21日，4（1）：59。 http://www.biomedcentral.com/1471-2105/4/59
参考文献----------References----------
data using co-inertia analysis. BMC Bioinformatics. 2003 Nov 21;4(1):59.
Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO: Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000, 24:227-235
Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN: A gene expression database for the molecular pharmacology of cancer.Nat Genet 2000, 24:236-244.
Weinstein JN, Mesirov JP, Lander ES, Golub TR: Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A 2001, 98:10787-10792.
Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17:520-525.
举例----------Examples----------
data(NCI60)
summary(NCI60)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-2-26 00:01:49
