In addition, DNA microarray experiments only interrogate transcriptionally-regulated genes, so it is inevitable that a significant portion of false positive and false negative interactions in an inferred network will be generated.
ChIP-chip experiments interrogating ERs of narrow width could be hindered by the combination of microarray design parameters with analytic approaches that require co-voting of spaced probes [2], [6], [7], [9]; for instance, 60 base oligonucleotides with a 200 300 base pair spacing are typical of many chromosomal tiling approaches (e.g. Agilent whole genome microarrays).
The results of the microarray experiments can be interactively interrogated in an on-line graphical GBrowse database at, where the fold ratio, number of observations for each gene, Student's t-test, Cyber-T p-values, XNG and NGO annotations, and the microarray probe locations can be visualized, and searched using chromosomal locations, gene names, or gene identifiers.
An advantage of using high throughput sequencing is the ability to interrogate gene expression without the representation bias present in microarray experiments.
We interrogated the GenitoUrinary Development Molecular Anatomy Project (http://www.gudmap.org/) and noted that Fras1 had been detected in certain expression microarray experiments using microdissected MM from E11 12 metanephroi.
The aim of our work was to propose a procedure to assess similarity between microarray experiments at the pathway level generating "Pathway signatures" (PS) for a set of experiments and use these signatures to interrogate microarray databases.
assisted in the microarray experiments.
Comparison of real-time RT-PCR and microarray experiments.
Microarray experiments were conducted according to the manufacturer's instructions.
I.F.K., H.-S.H. and A.M.M. performed microarray experiments.
