DeMAND - Revision history

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 ==References==
 <span id="Woo2015"></span>
 * Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.  ([http://www.ncbi.nlm.nih.gov/pubmed/26186195 PMID: 26186195]).

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 ==References==
 <span id="Woo2015"></span>
-* Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.  ([http://www.ncbi.nlm.nih.gov/pubmed/26186195 PMID: 26186195}).
+* Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.  ([http://www.ncbi.nlm.nih.gov/pubmed/26186195 PMID: 26186195]).
 <span id="Lefebvre2010"></span>
 * Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010)  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.  Mol Syst Biol.  '''6''':377. ([http://www.ncbi.nlm.nih.gov/pubmed/20531406 PMID: 20531406]).

@@ Line 72: / Line 72: @@
 ==References==
 <span id="Woo2015"></span>
-* Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.
+* Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.  ([http://www.ncbi.nlm.nih.gov/pubmed/26186195 PMID: 26186195}).
 <span id="Lefebvre2010"></span>
-* Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010)  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.  Mol Syst Biol.  '''6''':377. PMID: 20531406 ([http://www.ncbi.nlm.nih.gov/pubmed/20531406 link to paper]).
+* Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010)  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.  Mol Syst Biol.  '''6''':377. ([http://www.ncbi.nlm.nih.gov/pubmed/20531406 PMID: 20531406]).

← Older revision		Revision as of 20:05, 29 July 2015
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	<span id="Lefebvre2010"></span>		<span id="Lefebvre2010"></span>
−	* Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010) A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. 6:377. PMID: 20531406 ([http://www.ncbi.nlm.nih.gov/pubmed/20531406 link to paper]).	+	* Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010) A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. '''6''':377. PMID: 20531406 ([http://www.ncbi.nlm.nih.gov/pubmed/20531406 link to paper]).

@@ Line 72: / Line 72: @@
 ==References==
 <span id="Woo2015"></span>
-Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.
+* Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.
 <span id="Lefebvre2010"></span>
 * Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010)  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.  Mol Syst Biol.  6:377. PMID: 20531406 ([http://www.ncbi.nlm.nih.gov/pubmed/20531406 link to paper]).

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-The '''DeMAND''' (Drug Mode of Action through Network Dysreguation) [[#Bansal| [Bansal et al., manuscript in preparation]]] algorithm measures dysregulation between the expression of two genes in a network caused by e.g. a drug perturbation.  The list of top dysregulated gene pairs can reveal details of a drug's mode of action in the tested cellular system or tissue.
+The '''DeMAND''' (Drug Mode of Action through Network Dysreguation) [[#Woo2015| [Woo et al., 2015]]] algorithm measures dysregulation between the expression of two genes in a network caused by e.g. a drug perturbation.  The list of top dysregulated gene pairs can reveal details of a drug's mode of action in the tested cellular system or tissue.
-DeMAND is currently used with networks that integrate transcriptional (TF-target), post-translational (modulator-TF) and curated protein-protein interactions [[#Lefebvre2010 | [Lefebvre 2010]]].  Transcriptional interactions can be ascertained e.g. with the program ARACNe.  Post-translational interactions can be found using the program MINDy (command-line version).  Bayesian integration has been used to assemble final interactomes.
+DeMAND is currently used with networks that integrate transcriptional (TF-target), post-translational (modulator-TF) and curated protein-protein interactions [[#Lefebvre2010 | [Lefebvre et al., 2010]]].  Transcriptional interactions can be ascertained e.g. with the program ARACNe.  Post-translational interactions can be found using the program MINDy (command-line version).  Bayesian integration has been used to assemble final interactomes.
 Dysregulation is measured in the expression dataset for each pair of genes connected by an edge in the network.  It is determined by calculating the Kullback-Leibler (KL)-divergence of each pair.  The p-values for all dysregulated edges for each gene are then summed and corrected for number of interactions and dependence.  The resulting p-value per gene reflects the significance of dysregulation of each gene.
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 ==References==
 <span id="Woo2015"></span>
 Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation Analysis.  Cell '''162'''(2):441-51. doi: 10.1016/j.cell.2015.05.056.

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 ** Gene Symbol
 ** Chromosomal Location
-* A network (interactome) must be loaded (e.g. see [[ARACNe|ARACNe]] for producing a transcriptional network).
+* A network (interactome) must be loaded (e.g. see [[ARACNe|ARACNe]] for producing a transcriptional network).  See also [[File_Formats#Network_Formats |Network File Formats]] for more information.
 ==Data==