GMIEC

Welcome in GMIEC!! GMIEC is a framework that integrates omics data such as gene-expression, copy number variation, mutation, methylation and clinical data if available. At the level of the single patient, GMIEC identify group of genes (modules) that share common genomic features. Then, using an external database, the genes in each module are associated with their own target drugs. Therefore, GMIEC allows the identification, at the level of the single patient, of group of genes that are regulated by the same genetic/epigenetic regulator/s (e.g. TFs), sharing common genomic features and associated with different number of drugs.

Functionalities of GMIEC:

  • Identification of groups of genes with/without genomic alterations associated with drugs using gene-expression, copy-number alteration, methylation, mutation, clinical data;
  • Analysis using only the annotated genes;
  • Analysis using a custom list of genes;
  • Analysis using all genes between the datasets.

Functionalities of GMIEC-AN

  • Identification of group of genes with or without genomic alterations associated with drugs using predefined number of datasets;
  • Analysis using only the annotated genes;
  • Analysis using a custom list of genes;
  • Analysis using all genes between the datasets.

Functionalities of VIS-GMIEC:

  • Exploration of data at the level of single patient;
  • Summary of the scores, genes and drugs for the module genes at level of each patient.

Functionalities of GMIEC-RESULTS:

  • Parse the output of GMIEC and select only the modules given different criterias;
  • Visualize the results at the level of single patient.

Manual of GMIEC:

The manual is available on the official github repository of GMIEC-shiny: https://github.com/guidmt/GMIEC-shiny

Support:

Terms of use:

  • The features of GMIEC make it a tool that could be useful in the context of the data integration, data mining and data-exploration at the level of single patient. GMIEC is a tool that is provided only to perform analysis, exploratory analysis in basic and bioinformatic research with a scientific usage. GMIEC was not develop as tool to use in the clinical practice and authors decline each responsibility on its usage. See section terms of use for all details.

GMIEC - Input dataset (github.com/guidmt/GMIEC-shiny/tree/master/datasets)

GMIEC - Input annotation

GMIEC - Input drugs

GMIEC - Type of Analysis

GMIEC - Parameters Analysis

Analysis with minimum two datasets

Download

Upload results GMIEC

Heatmap scores drugs

Heatmap scores genes

Heatmap scores combined

Select a patient from the list

Select a module of the selected patient

Table summary scores for patients

Table summary genes module patient

Table summary drug module patient

GMIEC - Input dataset

Select patient

Heatmap module patient

Drugs in current module

Upload results GMIEC

Download
Terms of use

GMIEC is a Shiny application for the integration of omics data at level of single patient.

Copyright (C) 2020 Guidantonio Malagoli Tagliazucchi

This program is a free software. The user can redistribute and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

The features of GMIEC make it a tool that can be useful in the context of data integration, data mining and data-exploration at the level of single patient. GMIEC is a software that is provided only for research purpose. GMIEC was not developed as tool to use in the clinical practice and the authors decline every responsibility on its usage in clinics.

You may contact the author of this code, Guidantonio MT, at <guidantonio.mt AT gmail.com>