introduction to gene expression data

... Transferable.getTransferData() method If the data is represented by a DataFlavor that doesn’t correspond to a Java class (for example, plainTextFlavor), getTransferData() returns an InputStream for you to read the data ... StringSelection Methods Constructors public StringSelection(String data) # The constructor creates an instance of StringSelection containing data You can use this object to place the data on a clipboard ... Miscellaneous methods public DataFlavor[] getTransferDataFlavors() # The getTransferDataFlavors() method returns a two-element DataFlavor array consisting of DataFlavor.stringFlavor and DataFlavor.plainTextFlavor...

Ngày tải lên: 21/01/2014, 06:20

... reflects factors common to expression patterns in tumour response to drugs and in terms of their gene expression For these cell lines The median difference per gene between the two cell data sets, ... tubulin inhibitors, DNA-damaging agents, topoisomerase (Top1) inhibitors and topoisomerase (Top2) inhibitors The antimetabolite cluster included nine dihydrofolate reductase (DHFR) inhibitors (Df) ... of geneexpression profiling studies of the NCI60 cell lines Because the gene expression patterns were determined in untreated cells, our data relates to sensitivity to therapy, rather than to...

Ngày tải lên: 30/03/2014, 13:20

... difference between a data vector and all other data vectors in all clusters For any particular data vector v belonging to cluster A, let av be the average squared difference between data vector v and all ... [−1, 1] A value close to means the data vector is very probably assigned to the correct cluster, while a value close to −1 means the data vector is very probably assigned to the wrong cluster ... number of data vectors), and the standard deviation used to vary the individual vector values about their corresponding basis vectors Generally speaking, the standard deviation vectors were constructed...

Ngày tải lên: 22/06/2014, 00:20

... way to extract expression patterns in temporal gene expression data with continuous wavelet analysis It has been demonstrated that the application of wavelet transformation to gene temporal expression ... complex data sets are still emerging Because the unique feature of temporal gene expression data is autocorrelation between successive points, the immediate goals are to extract and to compare ... comparable to the length of the gene expression signal and therefore it extracts the low frequency trends of the signal In order to overcome the issue in temporal gene expression data analysis...

Ngày tải lên: 22/06/2014, 19:20

... and interpolated data Method (T-cell data) SSM on original data SSM on undersampled data SSM on interpolated data CoD on original data CoD on undersampled data CoD on interpolated data Edges inferred ... RESULTS Application to the GATA pathway To illustrate our approach (regime-SSM), we consider the embryonic kidney gene expression dataset [8] and study the set of genes known to have a possible ... there are N genes whose expression is related to a single process The ith gene s expression vector is denoted as gt(i) , t = 1, T, where T is the number of time points for which the data is available...

Ngày tải lên: 22/06/2014, 19:20

... was followed for INRArray 01.3 Eighty genes were added to the panel of 120 genes present on INRArray 01.2, leading to a total of 200 genes They were mainly genes involved in energy and xenobiotic ... time series gene expression data, ” Bioinformatics, vol 21, supplement 1, pp i159–i168, 2005 [7] C D Giurcˇ neanu, I Tˇ bus, and J Astola, “Clustering time a a ¸ series gene expression data based ... (through the second PC) but eigenvectors had to be checked to be smooth enough Too many oscillations in the eigenvectors could be irrelevant and potentially lead to misinterpretation 0.10 0.08 0.06...

Ngày tải lên: 22/06/2014, 19:20

... An application to microarray gene expression data Application of the LMC method to gene expression data is straightforward As an example of the application, we applied this method to cluster the ... that belong to very different categories are clustered together according to gene expression data Second, there is only a small number of genes presented in a microarray that are relevant to the biological ... here are designed to mimic microarray gene expression data in the way that each data point is a response series of expression values, and the distance or similarity between data points is measured...

Ngày tải lên: 23/06/2014, 01:20

... meaning 3 Chapter Introduction to Gene Expression Data 1.1 Gene Expression Deoxyribonucleic acid (DNA) is the central issues when learning to understand the gene expression Both DNA and RNA are ... regulatory network between genes, the so-called gene regulatory network A gene regulatory network shows the interaction between genes, thereby governing the rates at which genes are transcribed into ... regulatory factor binds to a particular gene and then regulates the expression level of this gene (Figure 2.5) This gene regulation is often context sensitive, e.g., gene A upregulates gene C,...

Ngày tải lên: 01/08/2014, 17:47

... expressed genes Selection of hypervariable (HV) genes To have an opportunity to evaluate inhomogeneity in gene expression variability, it is necessary to normalize this variability to make it ... binds peptides to present them to CTLs Signal transducer and activator of transcription 6, interleukin-4 induced; activates expression of the interleukin-4 receptor gene in response to interleukin-4 ... Rheumatol 1994, 21:1124-1127 Dozmorov I, Centola M: An associative of gene expression array data Bioinformatics 2003, 19:204-211 Rocke DM, Durbin B: A model for measurement error for gene expression...

Ngày tải lên: 09/08/2014, 01:23

... throughput data ExpressionPlot offers the gene expression community an easy -to- use tool for automated analysis of gene expression and RNA processing data The back end offers a solution to the problem ... plotted by this tool (Figure 2d; data in Additional file 3) Generation of plots and tables of changed genes/events The 2way tool and its associated table browser are the basic tools to examine the ... the table into other software, such as R or OpenOffice (or Excel), for automatic conversion of the genes into other IDs (such as Ensembl or Entrez), and for the automatic generation of expression- controlled...

Ngày tải lên: 09/08/2014, 23:20

... receptor signaling pathway 13.6 1.70E-03 Cytokine-cytokine receptor interaction NOD-like receptor signaling pathway 19.6 8.9 2.00E-09 5.30E-05 Toll-like receptor signaling pathway 32 Cytokine-cytokine ... expect to find the regulators of a gene, belonging to cluster B, in the gene pool of cluster A Thus, moving forward in our analysis we checked whether TV-DBN approach may recover known gene -to- gene ... evaluated with topological metrics as well as with available interactome data Also, we checked whether known gene -to- gene relationships could be retrieved from our cluster based approach Topological...

Ngày tải lên: 10/08/2014, 09:22

... compendia with microarray data from mouse tissues, including lung [17,18], were downloaded from the NCBI Gene Expression Omnibus repository To ensure consistent mapping between datasets, clone/probe ... same publication miR-145 is shown to selectively target genes that regulate the actin cytoskeleton, which is intimately coupled to cell migration Several target genes that regulate actin polymerization ... leukemia inhibitory factor (Chemicon International/Millipore, Billerica, MA, USA) EBs were generated by aggregation of stem cells in hanging drops in the absence of leukemia inhibitory factor, as described...

Ngày tải lên: 11/08/2014, 12:20

... complementary to more than 6,500 human genes We used 2,000 genes with the highest minimal intensity across the samples selected by [25] SRBCT The SRBCT data [5] contains gene- expression data from ... average expression value of gene m across all samples and across samples that only belong to class k respectively xi, m is the expression value of gene m in the ith sample.〚Á〛is the indicator function ... cross-validation on the Lung data and average the results obtained from 20 trials The Lung data contains 39 lung cancer samples with 18,117 gene expression levels This data set is classified into two categories,...

Ngày tải lên: 12/08/2014, 17:20

... for clustering gene expression data It is based on the idea that a group of genes tend to be clustered together if the distributions of gene expressions of these genes belong to the common Weibull ... complete data sets These three data sets were preprocessed by randomly removing 5-25% of the data in order to create the incomplete gene expression data sets, and the WDCM then was applied to these data ... one gene expression as a random variable, and construct the distribution of the gene expressions of gene i We then choose a subset of genes whose distributions of the gene expressions belong to...

Ngày tải lên: 12/08/2014, 17:20

... markers from heterogeneous collections of samples of DNA microarray data of gene expression We have applied this method to a highly heterogeneous set of stem cell gene expression data, with the objective ... uses large heterogeneous gene expression datasets to identify genes that can function as markers In summary, we examine the distribution of expression values of each probe set to identify gaps ... trying to identify coregulation or co -expression of genes in a series of samples that are relatively homogeneous In contrast, we are striving not to identify strict co -expression of many genes...

Ngày tải lên: 14/08/2014, 08:20

... factors We consider a data set with genes, the expression levels of which are measured using material from patients Note that the data consists of both the gene expression measurements and a data ... regulatory interactions between genes A gene has an 'indirect effect' on survival if its expression influences survival through one or more other prognostic genes present in the data A gene has ... subsequent text We have gene expression data for both genes from cancer patients and censored survival data from the same patients It is known that expression of PPARD influences expression of ADFP...

Ngày tải lên: 14/08/2014, 08:20

... not too many relative to the total number of detected genes Hence, controlling the FDR may be a reasonable strategy The non-Normality of gene- expression data hampers the ranking of the gene- expression ... all the genes, i.e., for 90% of the genes, a is larger than the usual denominator of the t-statistic ( s2 /n1 + s2 /n2 ) Although, adding a to the denominator avoids large t-statistics due to small ... analysis of appropriately transformed gene- expression data, either using Least Squares (LS, [12]) with homogeneous or heterogeneous error variance (heterogeneous error variance implies that a...

Ngày tải lên: 14/08/2014, 13:22

... to explore the effect of perturbing the gene- expression data for a single clustering algorithm [19] We have therefore designed a similar strategy to identify the consistently clustered gene- expression ... for the B-cell lymphoma data (Table 2) Robust clusters are therefore valuable for allowing a rapid 'drilling down' in a gene- expression dataset to groups of genes whose coexpression pattern is ... are able to group highly correlated data accurately, and that repeated measurements of gene- expression values can aid cluster partitioning [12] Nevertheless, even with such high gene- expression...

Ngày tải lên: 14/08/2014, 14:21

... enzyme inhibitors that reduce the activity of proteases (that is, enzymes catalyzing the hydrolysis of peptide bonds) (Table 4) Total Ordered Total Proteome Total For each data set, the *total number ... represent genuine and robust features of the data Absolute gene expression profiles for highly disordered proteins To differentiate modes of gene expression behavior among the highly disordered ... in the down-regulation of gene expression The absolute gene expression levels and the predicted miRNA regulation are anti-correlated The overall decrease in the gene expression of the transcripts...

Ngày tải lên: 14/08/2014, 21:20

... Outcome Data 23 V Sequencing of UGT1A1 Region 23 VI Gene Expression Analysis 26 DISCUSSION I Gene Expression in Paired Normal and Tumor Samples 29 II Gene Expression ... Diagnostic Cytology Laboratory 2005-2006 Cytotechnologist, Diagnostic Cytology Laboratory 2001-2005 Cytotechnologist, Borgess Medical Center 1999-2001 Lab Assistant, Parkview Hospital 1997-1998 Tutor, ... (TA)6TAA/(TA)6TAA (6/6) Chromatogram 24 Figure 11 Heterozygous (TA)6TAA/(TA)7TAA (6/7) Chromatogram Figure 12 Homozygous (TA)7TAA/(TA)7TAA (7/7) Chromatogram 25 VI Gene Expression Analysis Expression levels...

Ngày tải lên: 24/08/2014, 10:58