http://hipathia.babelomics.org/doc/ 2026-04-20T11:06:27+00:00 http://hipathia.babelomics.org/doc/ http://hipathia.babelomics.org/doc/lib/exe/fetch.php?media=logo.png text/html 2020-01-20T21:54:05+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=circuit_values&rev=1579557245&do=diff Circuit values Here you will find descriptive information about the matrix of circuit values. * Circuit values: You can download the matrix of circuit values by clicking on Circuit 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 discri… text/html 2024-02-27T13:17:45+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=data_format&rev=1709039865&do=diff Data format Different types of data are used in Hipathia. Some of this data require a certain structure explained on the following links: Note: The recommended file extensions are '.txt' or '.tsv'. Expression matrix file format Expression matrix file is a Tab-separated values file. text/html 2021-01-07T16:56:07+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=design_data&rev=1610038567&do=diff Design data panel The design data panel allows you to choose the kind of experiment you want to perform. You can choose between two kinds of experimental design: Two-group comparison The comparison is performed between the two groups described in the experimental design file. text/html 2018-12-26T21:08:58+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=differential_signaling_exercises&rev=1545858538&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 2021-01-29T22:14:30+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=differential_signaling&rev=1611958470&do=diff Differential signaling HiPathia allows inferring a value of signal transduction activity through any of the different circuits defined in any signaling pathway for each sample in the analyzed dataset, based on the gene expression values. Therefore, the same way that in a transcriptomic experiment differential expression between two conditions is conducted, HiPathia allows comparing the signal transduction activities between different conditions in a text/html 2024-02-27T13:33:41+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=experimental_design_file_format&rev=1709040821&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 Group_1 sample2 Group_1 sample3 Group_2 text/html 2020-02-20T16:26:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=expression_matrix_file_format&rev=1582215986&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 2017-05-24T13:54:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=filling_in_a_tool_form&rev=1495634056&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 2019-08-05T22:11:21+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=function_based_analysis&rev=1565043081&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 2021-01-07T16:52:59+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=function_level_analysis&rev=1610038379&do=diff Effector annotation source -Function level analysis-(Optional) If any of these checkboxes is selected, a differential functional activity analysis is performed. From a given gene expression profile, we estimate an effector proteins activation profiles and then we annotate each effector proteins using Gene ontology and Uniprot keywords annotation. text/html 2019-07-19T12:13:19+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=gene_list_file_format&rev=1563538399&do=diff Gene list file format Gene List is Tab-separated values file. This file has just one column, that is the Entrez ID of genes (1 Entrez ID per line). Here is an example of a file with 4 genes to be evaluated: Gene_1 Gene_2 Gene_3 Gene_4 text/html 2021-01-05T15:40:21+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=general_overview&rev=1609861221&do=diff General overview HiPathia is a web tool for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways. The web page is divided in two main areas: * The text/html 2024-02-27T11:42:11+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=how_to_cite_hipathia&rev=1709034131&do=diff How to cite HiPathia: Please, use the following convention to cite Hipathia tool: Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Comput Struct Biotechnol J. 2021 May 15;19:2968-2978. doi: 10.1016/j.csbj.2021.05.022. PMID: 34136096; PMCID: PMC8170118. text/html 2017-05-24T13:54:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=how_to_use_hipathia&rev=1495634056&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 2019-07-19T10:53:51+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=input_data_vafin&rev=1563533631&do=diff Input data A tabulated text file with data on genomic variation must be uploaded. This file must include list of gene names in HUGO or entrez id. This genes list corresponds to the genes to in silico knockdown simultaneously. text/html 2021-01-07T16:53:54+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=input_data&rev=1610038434&do=diff Input data panel In the input data panel, we must introduce the expression data. The expression data is a gene expression matrix provided by ourselves (see how to upload files in Upload your data). When we select a gene expression file, the number of samples of this matrix will appear under the text/html 2019-08-05T21:36:50+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=input_parameters&rev=1565041010&do=diff Input parameters Here you can visualize the parameters with which the current study was launched. * Species: The species of this experiment; Human (Homo sapiens),Mouse (Mus musculus) or Rat (Rattus norvegicus). * Expression file: The name of the expression file that has been used in the current study. text/html 2021-01-07T17:06:09+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=job_information&rev=1610039169&do=diff Study information This panel includes some parameters in order to identify and save our study. * Output folder: If we want to reorganize our studies we can select the folder in which we want save our report. By default the study will be saved in the home in a folder named text/html 2021-01-05T15:21:48+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=logging_in&rev=1609860108&do=diff Logging in In order to use the HiPathia pathway suite 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. See the tutorial * If you want to log in as an anonymous user, click on Start. text/html 2017-05-24T13:54:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=mutation_effect&rev=1495634056&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 2021-01-07T17:02:25+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=parameters&rev=1610038945&do=diff Experimental design This panel includes further parameters necessary to run a study. Paired Check to consider paired data in the analysis. When not selected the analysis is performed using unpaired parameter for the used statistical test-Wilcoxon-. Note: The Experimental design file must be ordered. text/html 2019-09-01T13:46:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=path_values&rev=1567345586&do=diff Circuit values Here you will find descriptive information about the matrix of circuit/path values. * Path values: You can download the matrix of circuit values by clicking on Path 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 discrim… text/html 2019-08-05T22:21:28+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=pathway_viewer&rev=1565043688&do=diff Pathway viewer A pathway viewer has been developed in order to make easier the visualization of the comparison results. You can select the pathway to see in the Categories list (1). You can also visualize a single circuit by clicking on its name ( text/html 2021-01-07T17:04:28+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=pathways&rev=1610039068&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. HiPathia retrieves pathway information from KEGG database. KEGG pathway database is a collection of manually drawn pathway maps representing the knowledge on the molecular interaction, reaction and relation networks. text/html 2019-08-08T13:37:12+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=perturbation_effect_results&rev=1565271432&do=diff Perturbation effect results Perturbation effect tool infers the effect of the knock-out or over-expression of a set of genes on the signaling pathways activity by comparing the signaling values of the pathways in the uploaded sample and the signaling values resulting from the modification of the expression values in the current sample by the selected values. text/html 2021-01-26T16:10:01+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=perturbation_effect&rev=1611677401&do=diff Perturbation effect The mechanistic model implemented in HiPathia can also be used for the simulation of the effect that interventions, such as gene knock-out and over-expression perturbations, can have over signaling pathways. This simulation is carried out by changing the expression level of the gene(s) of interest, recalculating the resulting signaling profile in the simulated condition and comparing it to the original profile. Similarly, the effect of inhibitory or agonistic drugs can be si… text/html 2017-05-24T13:54:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=prediction_exercises&rev=1495634056&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 2018-12-26T20:41:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=prediction_model&rev=1545856907&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 2021-01-30T14:22:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=prediction&rev=1612016536&do=diff Prediction The aim of the Prediction tool is to take advantage of the signalling circuit activities to distinguish between phenotypes (a two group comparison). HiPathia Prediction uses the signalling value of mechanism-based biomarkers to train a SVM prediction model with cross-validation-based techniques. Moreover, previously obtained models could be used to predict the phenotype of new samples. text/html 2021-01-22T19:39:47+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=sidebar&rev=1611344387&do=diff * What can HiPathia do for you * How to cite HiPathia * How to use HiPathia: * Logging in * General overview * Workflow * Upload your data * Data format * Expression matrix file format * Experimental design file format * Gene list file format * Tools: * Differential signaling * Prediction * Perturbation effect * Variant interpreter * Worked examples: * Worked example Differential signaling * Worked example Prediction * Worked … text/html 2021-01-07T16:56:45+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=species&rev=1610038605&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). text/html 2024-03-08T12:10:27+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=start&rev=1709899827&do=diff Welcome to HiPathia! HiPathia is a web tool for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways. HiPathia transforms uninformative gene expression and/or genomic variation data into signaling circuit activities, which carry information on the different cell functionalities triggered by them. Such signaling activities not only account for the underlying molecular mecha… text/html 2019-08-05T21:30:25+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=study_information&rev=1565040625&do=diff Study Information Here you can find the information about the selected study. * Name: the study name. * Description: the description of the current study. * Tool: the name of the used tool (in this case, is Hipathia). * Date: study's launching date (MM/DD/AAAA, HH:MM:SS AM/PM format) text/html 2017-05-24T13:54:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=type&rev=1495634056&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 HiPathia's server. text/html 2021-01-07T13:40:40+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=upload_your_data&rev=1610026840&do=diff Upload your data Follow the following steps to upload your data to HiPathia. 1- Either select the My data button in the upper bar of the HiPathia web or the File browser option of each pathway tool. 2- Your workspace folder will appear. 3- Select the folder in which you want to upload your data by navigating through your folders. Press the text/html 2021-01-11T13:41:59+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=vafin_exercises&rev=1610372519&do=diff Worked example Variant Interpreter Example 1: Fanconi Anemia study 1- Log in into HiPathia. For further information on this step visit Logging in. 2- We will work with expression data from custom tissue related to Fanconi Anemia (bone marrow derived cells). You can download the raw expression matrix used for this example from GEO repository, accession number text/html 2021-01-07T19:23:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=vafin&rev=1610047390&do=diff Variant Interpreter The Variant interpreter allows us to infer how a gene (or combination of genes) knockdown may deregulate the signaling pathways activity. This impact is evaluated by comparing the normal activity values from a given tissue, with the activity values of that same tissue calculated after the text/html 2021-01-05T15:49:15+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=what_can_do_hipathia_for_you&rev=1609861755&do=diff HiPathia, a mechanistic model of signaling pathways Mechanistic models offer a realistic framework to understand how signal transduction depends on changes in the expression of genes involved in signaling pathway circuits (see Hidalgo et al., 2017). Interestingly, cell signaling circuits trigger relevant cell functionalities (e.g., proliferation, cell death, metabolic changes, etc.), which virtually allows to estimate not only text/html 2021-01-28T21:23:48+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=worked_example_differential_example&rev=1611869028&do=diff Worked example Differential signaling The oestrogen receptor (ER+) positive group Vs negative group (ER-) Differential signaling inputs Note: You can also launch the Differential signaling example by clicking the Run example button or the help button on the header and then text/html 2024-02-27T13:31:40+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=worked_example_perturbation_effect&rev=1709040700&do=diff Worked example: Perturbation effect In silico simulations of the functional effects that drug-induced perturbations would have in the cell are extremely valuable to predict putative therapeutic impacts of drugs or combinations of them. They are also useful to evaluate response inconsistencies and to search for resistance mechanisms. To demonstrate the value of this tool, this example will be focused on the functional impact that the combined inhibition of text/html 2021-01-31T17:33:21+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=worked_example_prediction_train_and_test&rev=1612114401&do=diff Worked example prediction The most common prediction problem in biomedicine is related to class membership assignation. That is, given two known classes of individuals, defined by their attributes (e.g. gene expression profile), a predictor would be able of taking a new, unknown individual, and assigning to it a probability of belonging to one of these classes using its attribute information. text/html 2021-01-05T15:55:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=workflow&rev=1609862126&do=diff Workflow First step to use HiPathia is to be logged in. Please visit Logging in to further information on this step. HiPathia 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 HiPathia, please visit text/html 2021-01-19T17:37:01+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=workvafin&rev=1611077821&do=diff Worked example Variant Interpreter Diabetes study 1- Log in into HiPathia. For further information on this step visit Logging in. 2- We will work with expression data from custom tissue related to Diabetes. In this case we will work with a gene expression dataset of human islets from 63 donors (54 non-diabetic and 9 type 2 diabetic). You can download the raw expression matrix used for this example from GEO repository, accession number text/html 2020-12-30T21:14:23+00:00 Anonymous (anonymous@undisclosed.example.com) http://hipathia.babelomics.org/doc/doku.php?id=workvafin2&rev=1609362863&do=diff Worked example Variant Interpreter Example 1: Diabetes study 1- Log in into HiPathia. For further information on this step visit Logging in. 2- We will work with expression data from custom tissue related to Diabetes. In this case we will work with a gene expression dataset of human islets from 63 donors (54 non-diabetic and 9 type 2 diabetic). You can download the raw expression matrix used for this example from GEO repository, accession number