From fe1f8b4c028db727d35dff62305b84de0a33aeb9 Mon Sep 17 00:00:00 2001 From: Maria Marin Date: Mon, 1 Apr 2024 10:28:40 +0000 Subject: [PATCH] Add new file --- analysis/files/README.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 analysis/files/README.md diff --git a/analysis/files/README.md b/analysis/files/README.md new file mode 100644 index 0000000..5bb72d5 --- /dev/null +++ b/analysis/files/README.md @@ -0,0 +1,18 @@ +This directory includes the intermediate files used during the analysis: + +| NAME | DESCRIPTION | +|-----------------------|-------------------------------------------------------------------------------------------------| +| [Datos_Gppi.csv](https://medal.ctb.upm.es/internal/gitlab/disnet/network-medicine/network-medicine-for-schizophrenia/blob/master/analysis/files/Datos_Gppi.csv) | Protein ID, degree and Average Shortest Path Lenght of each node in the interactome | +| [Microarray_SCZ_metaanalysis_092017.csv](https://medal.ctb.upm.es/internal/gitlab/disnet/network-medicine/network-medicine-for-schizophrenia/blob/master/analysis/files/Microarray_SCZ_metaanalysis_092017.csv) | Results for the meta-analysis on the differential expression of genes in patients with schizophrenia, obtained from the supplementary material of the study of [Gandal et al. (2018)](https://www.science.org/doi/10.1126/science.aad6469) | +| [ Module_signif.csv](https://medal.ctb.upm.es/internal/gitlab/disnet/network-medicine/network-medicine-for-schizophrenia/blob/master/analysis/files/Module_signif.csv) | Number of seed genes, genes in interactome, genes in lcc and results of the statistical validation of the disease module for the pathologies with a significant disease module size | +| [dge_sorted.csv](https://medal.ctb.upm.es/internal/gitlab/disnet/network-medicine/network-medicine-for-schizophrenia/blob/master/analysis/files/dge_sorted.csv) | Genes with significantly higher or lower expression in schizophrenia patients after filtering [Microarray_SCZ_metaanalysis_092017.csv](https://medal.ctb.upm.es/internal/gitlab/disnet/network-medicine/network-medicine-for-schizophrenia/blob/ master/analysis/files/Microarray_SCZ_metaanalysis_092017.csv) file. Sorted by logFC (in absolute value) | +| [ drug_categories.csv ](https://medal.ctb.upm.es/internal/gitlab/disnet/network-medicine/network-medicine-for-schizophrenia/blob/master/analysis/files/drug_categories.csv) | Drug ID and its classification classified regarding the MeSH-pharmacological action (PA) therapeutic uses or its mechanism of action (MOA) | +| [ gandal_2018a_kMEs.csv](https://medal.ctb.upm.es/internal/gitlab/disnet/network-medicine/network-medicine-for-schizophrenia/blob/master/analysis/files/gandal_2018a_kMEs.csv) | Results of the co-expression module membership for each gene in PNDs, obtained from the supplementary material of the study of .[Lüscher et al. (2020)](https://www.nature.com/articles/s41398-020-0827-5). | + +Below are the intermediate files that have not been included in this directory due to their large size, as well as the link from which they can be obtained: + +| NAME | DESCRIPTION | LINK | +|-----------------------|----------------------------------------------------------------|-------------| +| [Closest distance.csv](https://drive.upm.es/s/lGXg33J3Rq0M0oa) | Results for the calculation of the closest distance between each disease - drug pair | https://drive.upm.es/s/lGXg33J3Rq0M0oa | +| [Closest_distance_rand.csv](https://drive.upm.es/s/aUK1BakJsRs6ckB) | Results for the mean and statistical deviation of the closest distance between each disease - drug pair, in comparison with 1,000 disease modules and sets of target proteins of each drug obtained randomly (degree preserving) | https://drive.upm.es/s/aUK1BakJsRs6ckB | +| [SPL PPI.csv](https://drive.upm.es/s/1RhbweyNYLTcCxF) | Shortest Path Length between each pair of proteins in the interactome | https://drive.upm.es/s/1RhbweyNYLTcCxF | \ No newline at end of file -- 2.24.1