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Especially, this limitation would be serious when analyzing multiple tissue data.
Especially, this problem should be serious when analyzing a diverse gene expression data set like a multiple tissue data set.
The other is a human multiple tissue data set, which has been subjected to a number of single sample-targeting methods [1] [3], [5].
Especially, by focusing on the results for the multiple tissue data set, we found that the BEEM approach is positioned between the two others.
On the other hand, the multiple tissue data set from various types of tissues seems to have more heterogeneous transcriptomes, and closes to the bicluster model.
For the multiple tissue data set, the performance of BEEM depends on the type of input gene set libraries; SSA works better for the TF binding motif gene set library while BEEM works better for the curated gene set library.
Similar(50)
We downloaded two microarray data sets from the GEO database: a human breast cancer data set (GSE3494) [13] and a human multiple tissues data set (GSE1133) [1].
The silkworm genome contains about 14,623 genes and larvae multiple tissue transcriptional data were obtained using a 22,987 oligonucleotide probe microarray [19] [21].
By applying BEEM to the TF binding motif gene sets and multiple tissue expression data set, we assigned a p-value to each gene set.
Multiple tissue expression data from day 3 of the fifth instar showed that 1,403 of the 2,436 induced genes have multiple tissue expression, indicating that almost all of the silkworm tissues were affected by the infection [19].
To validate this hypothesis, we focused on the distribution of the sizes of positive gene sets retrieved by each method, especially the result for the multiple tissue expression data set and curated gene set library (because, for this input combination, all the three methods have a number of positive gene sets of diverse sizes).
More suggestions(15)
multiple tissue interfaces
multiple tissue interactions
multiple tissue samples
multiple tissue lineages
multiple tissue layers
multiple tissue types
multiple tissue specimens
multiple tissue boxes
multiple imputation data
multiple tissue defects
multiple tissue sections
multiple tissue banks
multiple tissue biopsies
multiple tissue punches
multiple tissue characteristics
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