Analyzing time series gene expression data
Citations
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Cites background from "Analyzing time series gene expressi..."
...Besides biclustering along the gene-sample dimensions, there has been a lot of interest in mining gene expression patterns across time [4]....
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...[4] Z. Bar-Joseph....
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...For a more comprehensive look at time-series gene expression analysis, see the recent paper by Bar-Joseph [4]....
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...For a more comprehensive look at time-series gene expression analysis, see the recent paper by Bar-Joseph [4]....
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207 citations
Cites methods from "Analyzing time series gene expressi..."
...Although LSA had its roots grounded in microbial community analysis, the technique can be readily applied to other biological time series data, such as replicated gene expression time series data from microarray and RNASeq experiments [27-29]....
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References
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"Analyzing time series gene expressi..." refers background in this paper
...Many algorithms have been introduced for identifying genes differentially expressed between two experiments in the static expression case (Golub et al., 1999; Dudiot et al., 2004)....
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5,176 citations
"Analyzing time series gene expressi..." refers background or methods in this paper
...Some of the time series experiments are performed to detect periodic genes (Spellman et al., 1998)....
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...…clustering was used to determine function for unknown genes (Eisen et al., 1998), to look at expression programs for different systems in the cell (Spellman et al., 1998) and for identifying sets of genes that are specifically involved in a certain type of cancer or other diseases (Alon et al.,…...
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..., 1998), to look at expression programs for different systems in the cell (Spellman et al., 1998) and for identifying sets of genes that are specifically involved in a certain type of cancer or other diseases (Alon et al....
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...the three alpha cell cycle experiments (Spellman et al., 1998; Zhu et al., 2000; Pramilla et al., 2002) were sampled every 7, 15 and 10 min, respectively]....
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...WT alpha (Spellman et al., 1998) Alpha mating factor 0–119 64 Every 7 min...
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4,836 citations
"Analyzing time series gene expressi..." refers background or methods in this paper
...These include cell cycle double knockouts (Zhu et al., 2000; Pramilla et al., 2002) and knockouts under stress conditions (Gasch et al., 2000)....
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...These methods include cluster analysis (Zhu et al., 2000; Gasch et al., 2000), in which clusters of genes are compared across the two experiments and generalized singular value decomposition (SVD) [presented by Alter et al. (2003)], which are also used to detect differences between sets of genes,…...
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..., 2002) and knockouts under stress conditions (Gasch et al., 2000)....
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...These methods include cluster analysis (Zhu et al., 2000; Gasch et al., 2000), in which clusters of genes are compared across the two experiments and generalized singular value decomposition (SVD) [presented by Alter et al....
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..., 2002) and stress (Gasch et al., 2000)], they react by activating a new expression program....
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4,131 citations