Differences

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--- what_can_do_hipathia_for_you [2015/12/18 15:49] – mhidalgo
+++ what_can_do_hipathia_for_you [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== What can do HiPathia for you ======
+====== What can do Metabolizer for you ======
-HiPathia integrates two different pathway tools:
+Metabolizer integrates three different pathway tools:
-  * **Differential signaling** allows us to see how cell signaling changes in different conditions.
+  * **Activity** allows you to see how module activity changes in different conditions.
-  * **Prediction** allows us to train a prediction test and test it with different data.
+  * **Knockout** allows you to simulate knockouts or over-expressions of one or several genes or the effect of drugs in metabolic module genes.
+  * **Prediction** allows you to train a prediction model and test it with different data.
-HiPathia is able to integrate different technologies to produce an accurate result.
+Metabolizer is able to integrate RNA-Seq and microarray data to produce an accurate result.
-===== Differential signaling =====
+===== Activity =====
-HiPathia allows us to compute a signal value for each signaling path and each one of our data samples.
+Metabolizer-Activity allows you to compute activity (overall flux) of each metabolic module and each one of your data samples.
-Therefore, it allows us to **compare** the signal value:
+Therefore, it allows you to **compare** the activity values:
-  * Between two groups, in order to see which signaling paths change and how, or
+  * Between two groups, in order to see which modules are changed and how
-  * With a continuous value, giving us the correlation of each signaling path with this variable.
-HiPathia is able to integrate **variant files** in order to compute a more accurate estimation of the samples expression.
+In order to check how to use these options please see [[differential_signaling|Activity]].
-This integration can be done in order to:
-  * Have a more precise expression profile of the samples we are comparing, or
-  * Check the effect on the signaling pathways of the mutations in the genome.
-In order to check how to use these options please see [[how_to_use_hipathia|How to use HiPathia]].
+===== Knockout =====
+Metabolizer-Knockout allows you to modify the expression value of a set of genes and then check the effect of this change at the level of module activity. In this way, you can simulate effect of knockouts (KO) and over-expressions of one or several genes or the effect of drug(s) in the activity of metabolic modules.
+The simulations can be done:
+  * Using single sample: This option calculates fold-change of module activity between after and before KO/OE.
+  * Using multiple samples: This option uses one selected sample to calculate effect of in-silico intervention of gene expression on module activity. Rest of the samples are used to train a prediction model. Metabolizer uses this trained model to calculate class probability of selected sample including before and after intervention.
+  * User can use the options above by selecting single/multiple genes or drug(s) on interactive pathway panel. Metabolizer also allows to auto-KOs. Auto-KOs option calculates effect of simple KOs using all module genes by one by.
+In order to check how to use these options please see [[in-silico_knockout:over_expression| Knockout]].
 ===== Prediction =====
-HiPathia allows us to train, download and test a prediction model for our dataset. The model can be trained either to:
+Metabolizer allows you to train, download and test a prediction model for your dataset using different machine learning algorithms. Prediction can be done using following methods; [[https://en.wikipedia.org/wiki/Support_vector_machine|SVM]], [[https://en.wikipedia.org/wiki/Random_forest|Random Forest]].
-  * Discriminate between two different groups of samples, or
+The model can be trained and test:
-  * Predict the value of an unknown variable.
+  * Using different groups (2 and more groups) of samples.
-In order to check how to use these options please see [[how_to_use_hipathia|How to use HiPathia]].
+In order to check how to use these options please see [[prediction|Prediction]].