Metabolizer

how_to_cite_metabolizer

ccubuk (ccubuk@undisclosed.example.com) — 2019-03-15T14:14:41+00:00

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.

sidebar

ccubuk (ccubuk@undisclosed.example.com) — 2018-11-07T13:29:23+00:00

* 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…

expression_matrix_file_format

ccubuk (ccubuk@undisclosed.example.com) — 2017-03-10T11:46:41+00:00

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.

general_overview - [Upper bar]

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:59:44+00:00

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.

worked_example_differential_example

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:58:15+00:00

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:

worked_example_prediction

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:54:30+00:00

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:

brca_1_sample_test.txt - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:53:45+00:00

brca_2_sample_test.txt - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:44:24+00:00

worked_example_prediction_-_train

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:37:23+00:00

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:

worked_example_knockout

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:37:04+00:00

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:

brca_example1_40_design.txt - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:35:56+00:00

brca_example1_40_exp.txt - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-29T23:35:14+00:00

metabolizer_ko_16.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-26T12:19:09+00:00

metabolizer_ko_15.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-26T12:18:50+00:00

metabolizer_interactive_page.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-26T12:15:10+00:00

metabolizer_ko_3_4.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-26T12:14:16+00:00

metabolizer_ko_1_2.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-26T12:13:29+00:00

knockout3.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-23T02:53:55+00:00

knockout2.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-23T02:48:07+00:00

knockout.png - created

ccubuk (ccubuk@undisclosed.example.com) — 2016-12-23T02:43:25+00:00