http://metabolizer.babelomics.org/doc/ 2026-04-18T11:22:02+00:00 http://metabolizer.babelomics.org/doc/ http://metabolizer.babelomics.org/doc/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=design_data&rev=1495636426&do=diff Design data panel The design data panel allows you to choose groups which you want to compare. The experimental design file must include two columns: the first one with the names of the samples, the second one with the class to which each sample belongs. See how to upload files in text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=differential_signaling_exercises&rev=1495636426&do=diff Differential signaling exercises In this page you will find different exercises for further practising in the use of the HiPathia Differentail Signaling tool. Try to answer the questions using the results given by HiPathia for each case. To see how to use the application please visit the text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=differential_signaling&rev=1495636426&do=diff Module Activity Metabolizer allows us to compute activity value for each module and each one of our data samples. Therefore, it allows us to compare the module activity value between different conditions. The tool can be accessed from the main menu bar, by clicking on the text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=experimental_design_file_format&rev=1495636427&do=diff Experimental design file format Experimental design is Tab-separated values file. This file has two columns, the first one corresponds to the sample name and the second one corresponds to the phenotype. sample1 Cancer sample2 Cancer sample3 Healthy sample4 Healthy text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=expression_matrix_file_format&rev=1495636426&do=diff Expression matrix file format Expression matrix file is a Tab-separated values file. A tab-separated values (TSV) file is a simple text format for storing data in a tabular structure (e.g. database or spreadsheet data). Each record in the table is one line of the text file. Each field value of a record is separated from the next by a tab stop character. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=filling_in_a_tool_form&rev=1495636426&do=diff Filling in a tool form HiPathia integrates two different pathway tools: Differential signaling and Prediction. Both pathway tools can be accessed from the main menu bar, by clicking on their respective names (see Workflow). The main page of a pathway tool is its filling in form. This form includes all the information and parameters that the tool needs to process a job. The form is divided in different panels: text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=function_based_analysis&rev=1495636426&do=diff Function based analysis For each of the functional analysis selected to be performed, the same descriptive statistics as in the Path values case are shown: * GO terms/Uniprot keywords values: You can download the matrix of function values by clicking on text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=function_level_analysis&rev=1495636426&do=diff Function level analysis If any of these checkboxes is selected, a functional analysis is performed. * Gene ontology: a functional analysis with annotations of Gene Ontology is performed. * Uniprot keywords: a functional analysis with annotations of Uniprot keywords is performed. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=general_overview&rev=1495636426&do=diff General overview Metabolizer is a web tool for analysis of modular architecture of metabolic pathways using transcriptomic data. The web page is divided in two main areas: * The Upper bar: In this bar we can find different buttons to interact with the web tool. text/html 2019-03-15T14:14:41+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=how_to_cite_metabolizer&rev=1552659281&do=diff How to cite Metabolizer Please, use the following convention to cite Metabolizer tool: Cubuk, C., Hidalgo, M., Amadoz, A., Rian, K., Salavert, F., Pujana, M., Mateo, F., Herranz, C., Carbonell-Caballero, J. and Dopazo, J. (2019). Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. npj Systems Biology and Applications, 5(1), doi: 10.1038/s41540-019-0087-2. text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=how_to_use_hipathia&rev=1495636427&do=diff How to use HiPathia HiPathia can be used mainly in two different ways: * Differential signaling allows us to see how cell signaling changes in different conditions. * Prediction allows us to train a prediction test and test it with different data. text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=input_data&rev=1495636427&do=diff Input data panel In the input data panel, we must introduce the Expression Data. See how to upload files in Upload your data. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=input_parameters_prediction_test&rev=1495636426&do=diff Input parameters * Expression file: Expression file of the current job. * Species: Species file of the current job. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=input_parameters_prediction&rev=1495636426&do=diff Input parameters Here you can visualize the parameters with which the current job was launched. * Expression file: Expression file of the current job. * Design file: Design file of the current job. * Comparison: The groups that have been compared text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=input_parameters&rev=1495636426&do=diff Input parameters Here you can visualize the parameters with which the current job was launched. * Expression file: Expression file of the current job. * Design file: Design file of the current job. * Comparison: The groups that have been compared text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=job_information&rev=1495636426&do=diff Job information This panel includes some parameters in order to identify and save our job. * Output folder: We must select the folder in which we want our data to be saved. * Job name: We can give a name to our job. This is very useful to later identify it among the other jobs listed in the text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=logging_in&rev=1495636426&do=diff Logging in In order to use the Metabolizer you need to be logged in. If you do not have an account, you can either create a new user for you or log in as an anonymous user. * If you want to log in as an anonymous user, click on Start. * If you already have an account, log in by clicking on text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=mutation_effect&rev=1495636426&do=diff Mutation impact This panel only appears when a VCF file has been selected. In this case, we need to specify some further parameters: * Reference genome: Select either reference genome GRCh37 or GRCh38 * Inheritance pattern: Select the kind of inheritance pattern, either recessive or dominant. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=parameters&rev=1495636426&do=diff Parameters panel This panel includes further parameters necessary to run a job. Decompose paths: Check to consider subpathways with a unique input and a unique output in the analysis. When not selected the analysis is performed using subpathways with multiple inputs but a unique output (effector subpathways). text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=path_values_prediction_test&rev=1495636426&do=diff Module Values * Module values: You can download the matrix of module activity values of test dataset by clicking on Module Activity Values. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=path_values_prediction&rev=1495636426&do=diff Module Values * Module values: You can download the matrix of module activity values by clicking on Module Values. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=path_values&rev=1495636426&do=diff Module Values Here you will find descriptive information about the section of Module Values. * Module values: You can download the matrix of module activity values by clicking on Module Values. * Heatmap: A heatmap is a graphical representation of the values of a matrix. A not-supervised clustering is performed on the data per columns (samples). A good separation between the two colors of the upper bar of the heatmap indicates that the differences between the two groups are big enough to d… text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=pathway_viewer&rev=1495636426&do=diff Pathway viewer A pathway viewer has been develop in order to make easier the visualization of the comparison results. You can select the pathway to see in the Pathways list (1). You can also visualize a single circuit by clicking on its name (3) in the text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=pathways&rev=1495636427&do=diff Pathways This panel includes the list of all available pathways in HiPathia. We can select the pathways with which the analysis will be performed. By default all available pathways are selected. text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=prediction_exercises&rev=1495636427&do=diff Differential signaling exercises In this page you will find different exercises for further practising in the use of the HiPathia Prediction tool. Try to answer the questions using the results given by HiPathia for each case. To see how to use the application please visit the text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=prediction_model&rev=1495636427&do=diff Prediction model Here you can visualize the results from the prediction analysis. * K-fold cross-validation: The number of equal sized subsamples in which the original sample is randomly partitioned. * Model statistics: You can download the model statistics. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=prediction_results&rev=1495636426&do=diff Prediction Results * Prediction: You can download the matrix of predicted classes of test samples by clicking on Prediction results. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=prediction&rev=1495636426&do=diff Prediction Train The aim of the Prediction tool is to take advantage of the module activities to distinguish between phenotypes. Metabolizer Prediction uses the module activity values to compute a RF or SVM prediction model with cross-validation. Moreover, previously obtained models can be used to predict the phenotype of new samples. text/html 2018-11-07T13:29:23+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=sidebar&rev=1541597363&do=diff * What can do Metabolizer for you * How to cite Metabolizer * How to use Metabolizer: * Logging in * General overview * Workflow * Upload your data * Expression matrix file format * Experimental design file format * Tools: * Activity * Knockout * Prediction * Worked examples: * Worked example Differential Module Activity * Worked example Differential Module Activity * Worked example Knockout * Worked example Prediction - Train * Worked exampl… text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=species&rev=1495636426&do=diff Species Here we must choose the species of our experiment. You can choose among: * Human (Homo sapiens) * Mouse (Mus musculus) * Rat (Rattus norvegicus) * Zebrafish (Danio rerio) * Fruit fly (Drosophila melanogaster) * Worm (Caenorhabditis elegans) text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=start&rev=1495636426&do=diff Welcome to Metabolizer! Metabolizer is a web tool for analysis of modular architecture of metabolic pathways using transcriptomic data. Metabolizer calculates impact of modules on production of metabolites.These modules are conserved part of metabolism which starts with substrate(s) and ends with a product. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=train_method&rev=1495636426&do=diff Train Method The method panel allows you to choose a learning algorithm. 2 well established machine learning algorithms exist; Random Forest and Support Vector Machines. * Random Forest (RF): Random forests or random decision forests are an ensemble learning method for classification, regression and other tasks, that operate by constructing a multitude of decision trees at training time and outputting the class that is the mode of the classes (classification) or mean prediction (regression) o… text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=type&rev=1495636426&do=diff Type panel The type panel allows you to choose the kind of prediction analysis you want to perform. You can choose between two options: * Train new model: A prediction model is generated with your selected data. * Test existing model: You can choose an already trained model to predict the phenotype of new samples. Existing prediction models can be selected from your project folders stored in Metabolizer's server. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=upload_your_data&rev=1495636426&do=diff Upload your data Follow the following steps to upload your data to Metabolizer. 1- Either select the My data button (1) in the upper bar of the Metabolizer web or the File browser (7) option of each pathway tool. 2- Your workspace folder (2) will appear. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=what_can_do_hipathia_for_you&rev=1495636426&do=diff What can do Metabolizer for you Metabolizer integrates three different pathway tools: * Activity allows you to see how module activity changes in different conditions. * Knockout allows you to simulate knockouts or over-expressions of one or several genes or the effect of drugs in metabolic module genes. text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=worked_example_differential_example&rev=1495636426&do=diff Worked example Differential Module Activity 1- Log in into Metabolizer. For further information on this step visit Logging in. 2- We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix and the experimental design from these links: text/html 2017-05-24T14:33:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=worked_example_knockout&rev=1495636427&do=diff Worked example Knockout 1- Log in into Metabolizer. For further information on this step visit Logging in. 2- We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix and the experimental design from these links: text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=worked_example_prediction_-_train&rev=1495636426&do=diff Worked example Prediction - Train 1. Log in into Metabolizer. For further information on this step visit Logging in. 2. We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix and the experimental design from these links: text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=worked_example_prediction&rev=1495636426&do=diff Worked example Prediction - Test 1. Log in into Metabolizer. For further information on this step visit Logging in. 2. We will test the model with another Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix of the test data (one of them) from the link: text/html 2017-05-24T14:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://metabolizer.babelomics.org/doc/doku.php?id=workflow&rev=1495636426&do=diff Workflow First step to use Metabolizer is to be logged in. Please visit Logging in to further information on this step. Metabolizer data is arranged in folders as in a personal computer. You can upload data to any folder and organize it as desired (1). To learn how to upload data to Metabolizer, please visit