An overview of image-processing methods for Affymetrix GeneChips

We present an overview of image-processing methods for Affymetrix GeneChips. All GeneChips are affected to some extent by spatially coherent defects and image processing has a number of potential impacts on the downstream analysis of GeneChip data. Fortunately, there are now a number of robust and accurate algorithms, which identify the most disabling defects. One group of algorithms concentrate on the transformation from the original hybridisation DAT image to the representative CEL file. Another set uses dedicated pattern recognition routines to detect different types of hybridisation defect in replicates. A third type exploits the information provided by public repositories of GeneChips (such as GEO). The use of these algorithms improves the sensitivity of GeneChips, and should be a prerequisite for studies in which there are only few probes per relevant biological signal, such as exon arrays and SNP chips.     

Bolkian and Bokian Retardation in Homo Sapiens

Although a low genetic barrier is said to separate humans from apes, Homo sapiens is characterized by striking developmental and anatomical particularities. On the one hand, humans have a very extended life history (retardation). On the other hand, human anatomy shows many instances of both neoteny and hypermorphosis.In 1918, Bolk proposed his 'retardation theory' that links both aspects of the human condition. We show in this paper that his theory becomes surprisingly powerful when Bolk's retardation principle is applied to generalized developmental gradients (such as the cephalocaudal gradient that dominates overall ontogeny). In this way, the main particularities of the human body (extended life history; long limbs, and very long legs; very low brachial and crural indices; highly developed pollex and hallux; reduced prognathism; advanced telencephalization etc.) can be reduced to a single developmental matrix.In 1926, Bok noted that, in a series of equivalent organs (such as the finger row), the ontogenetic latecomer tends to be more neotenic than a corresponding forerunner. We show that Bok's observation is a logical corollary of Bolk's retardation theory and that it is important for understanding some pecularities of human anatomy such as the pronounced differentiation between hands and feet.     

Motif effects in Affymetrix GeneChips seriously affect probe intensities

An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch.     

An application for assessing quality of RNA hybridized to Affymetrix GeneChips

This paper describes a stand-alone application for estimating the 3' to 5' ratio by fitting a mixed effects model to the interior pixel intensities of perfect match probes for selected control probe sets from an Affymetrix *.DAT file. The effectiveness of this method was demonstrated previously by an application of the method to two microarray datasets for which external verification of RNA quality was known. This application provides a more objective assessment of sample quality in that both a point estimate and 95% confidence interval about the 3' to 5' ratio are provided. AVAILABILITY: The software and installation instructions are freely available for download at http://www.people.vcu.edu/~kjarcher/Research/Data.htm     

Assessing the Quality of Hybridized RNA in Affymetrix GeneChips Using Linear Regression

The quality of data from microarray analysis is highly dependent on the quality of RNA. Because of the lability of RNA, steps involved in tissue sampling, RNA purification, and RNA storage are known to potentially lead to the degradation of RNAs; therefore, assessment of RNA quality and integrity is essential. Existing methods for estimating the quality of RNA hybridized to a GeneChip either suffer from subjectivity or are inefficient in performance. To overcome these drawbacks, we propose a linear regression method for assessing RNA quality for a hybridized Genechip. In particular, our approach used the probe intensities from the .cel files that the Affymetrix software associates with each microarray. The effectiveness and the improvements of the proposed method over the existing methods are illustrated by the application of the method to the previously published 19 human Affymetrix microarray data sets for which external verification of RNA quality is available.     

Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

Background  

Affymetrix GeneChip technology enables the parallel observations of tens of thousands of genes. It is important that the probe set annotations are reliable so that biological inferences can be made about genes which undergo differential expression. Probe sets representing the same gene might be expected to show similar fold changes/z-scores, however this is in fact not the case.     

人（Homo sapiens）海马神经元microRNA调控网络的构建及其基本性质研究

目的：建立人海马神经元中的分子相互作用调控网络,研究miRNA在这个网络中是如何与其他信号通路相互作用并形成更复杂的生物网络,以及miRNA对网络中其靶点的调控如何影响生物网络的性质。方法：通过对已发表文献实验数据的挖掘分析,获得了哺乳动物海马神经元中主要信号通路的580个组分的一组相互作用数据,以及海马神经元中的miRNA表达谱。使用PITA,Miranda,TargetScan三个miRNA靶点预测软件计算出了这580个组分中的345个miRNA靶点。使用cytoscape对这些相互作用数据建立网络并对其性质进行计算分析。结果：建成了海马神经元中一个包含633个节点1653条边的miRNA调控网络,该网络中转录因子,adapter,酶更多的受到miRNA调控。结论：人海马神经元中,miRNA主要通过对转录因子,adapter和酶进行调控,与其他信号通路相互作用形成了一个更加复杂的网络,新形成的网络的集群系数,网络异质性,网络中心化程度,平均最短路径长度,平均邻点数都发生了变化。     

Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips

MOTIVATION: Affymetrix GeneChips are common 3' profiling platforms for quantifying gene expression. Using publicly available datasets of expression profiles from human and mouse experiments, we sought to characterize features of GeneChip data to better compare and evaluate analyses for differential expression, regulation and clustering. We uncovered an unexpected order dependence in expression data that holds across a variety of chips in both human and mouse data. RESULTS: Order dependence among GeneChips affected relative expression measures pre-processed and normalized with the Affymetrix MAS5.0 algorithm and the robust multi-array average summarization method. The effect strongly influenced detection calls and tests for differential expression and can potentially significantly bias experimental results based on GeneChip profiling.     

Rational Preselection from Hamadryas to Homo Sapiens: The Place of Decisions in Adaptive Process

Normally biological and sociocultural evolution are explained in terms of blind variation and selective retention. This theory avoids intrinsic teleological fallacies but fails to account for a type of purposive behavior that is both distinctive and adaptively significant. The preselective hypothesis advanced here asserts that certain highly social animals including Homo sapiens are able to anticipate complex evolutionary problems. They may then beat natural selection to the draw by making their own deliberate adaptive choices, where the advantage of doing so is perceptually obvious. Such decisions occur both at the individual level and through political processes at the group level. Especially in group preselection, the result is an adaptive mechanism of unparalleled flexibility and rapidity of action, one very inadequately accounted for by ethnologists. Implications are suggested for ethology, archaeology, and ethnology in terms of redefining culture and revising models of cultural adaptation and evolution to make the study of process more effective . [evolutionary theory, cultural ecology, decision process, ethology, cognition]     

人类基因的剪接受体位点的识别方法与应用研究

本文针对人类剪接位点数据库研究,发现剪接受体位点左侧内含子30碱基内存在明显特征信息．利用李雅普诺夫定理建立识别新方法,识别准确率80％,方法简单易行,这些对基因识别和内含子功能研究有重要的参考依据．     

LIM结构域蛋白FHL1C抑制Notch信号途径的转录激活研究

目的：克隆人表达FHL1C基因以及建立真核表达载体和慢病毒载体。方法：从人的骨骼肌细胞来源的cDNA中扩增并克隆人FHL1C基因的编码区,连接至pMD-18T载体酶切鉴定后测序。序列测定确认后,双酶切pMD18T-FHL1C回收片段,插入真核表达载体,构建真核表达载体pCMV-Myc-FHL1C酶切鉴定正确后,转染Hela细胞及Cos7细胞,用Western Blot检测其在转染细胞中的表达,用双荧光素报告基因系统检测其对Notch信号作用。构建FHL1C-IRES-GFP表达单元,建立慢病毒表达载体plen-ti6/V5-FHL1C-IRES-GFP,包装慢病毒后感染培养的细胞,用免疫荧光显微镜、Western Blot检测分析其在被感染的细胞中的表达。结果：通过PCR方法成功扩增了人FHL1C基因的编码区。通过转染Hela及Cos7细胞,使用Western Blot检测其蛋白水平表达,双荧光报告基因系统分析均能够下调激活的Notch信号。成功构建了FHL1C慢病毒表达载体pLenti6/V5-FHL1C-IRES-GFP,包装慢病毒,把获取的慢病毒感染细胞后通过荧光显微镜证实被感染的细胞绿色荧光蛋白正确表达,Western Blot检测证实其表达。结论：成功建立起FHL1C真核表达载体及慢病毒表达系统,为研究急性T淋巴细胞白血病与Notch信号转导通路之间的关系奠定了基础。