Web Portal for searching samples from BCNTB
- index.php
- header.php
- body.php
- ccle.php
- tgca.php
- data_returned.php
- request.php
- data
- SF2BiomartMapping.txt
- SF2MinerMapping.txt
- ccle_cn.csv
- ccle_cn_target_with_chr.csv
- ccle_gea_target.txt
- ccle_gene_exp.csv
- ccle_gene_list.txt
- ccle_mut.csv
- dr_gea_target.txt
- dr_gene_list.txt
- dr_gene_list_mut.txt
- dr_mut_exp.txt
- dr_mut_target.txt
- pam50.genes.txt
- tcga_gea_target.txt
- tcga_gene_list.txt
- mentha.txt
- tcga_gene_exp.csv
- images
- data
- js
- scripts
- ExecQuery.php
- LaunchCommand.php
- LoadCCLEAnalysis.php
- LoadDRAnalysis.php
- LoadStatisticalDetails.php
- LoadTCGAAnalysis.php
- PHPMailer.php
- PerformRequest.php
- RetrieveCCLEDatasets.php
- RetrieveDRDatasets.php
- RetrieveGeneList.php
- RetrievePublications.php
- RetrieveTCGADatasets.php
- RetrieveTableFeatures.php
- conn_details.php
- functions.php
- res_mixed.php
- res_rnaseq.php
- res_wgs.php
- vars.php
- styles
For further details please refer to the comments inside the code
| File name | Description |
|---|---|
| index.php | This is the main home page. It includes 3 other pages (header, body, footer) |
| header.php | The header contains the html "head" section, with all the links to CSS files and JS plugins |
| body.php | The body page contains the logo, breadcrumb, and the main filtering section |
| data_returned.php | Analysis page for the data collected inside the BCNTB |
| tcga.php | Analysis page for The Cancer Genome Atlas data |
| ccle.php | Analysis page for data extracted from the Cancer Cell Line Enciclopedia |
| request.php | Web page where interested users can proceed to request selected samples |
| scrips/res_mixed.php | Page of analyses if returned data are from mixed technologies (wgs and rna-seq) |
| scrips/res_rnaseq.php | Page of analyses if returned data are from RNA-seq technology |
| scrips/res_wgs.php | Page of analyses if returned data are from WGS technology |
| File name | Description |
|---|---|
| ExecQuery.php | This is the most important script. Based on what selected, it performs multiple queries to the BCNTB database and retrieve the results |
| RetrieveCCLEDatasets.php | Retrieve the samples from CCLE, according to the features selected in the main page |
| RetrieveDRDatasets.php | Retrieve the samples from returned data, according to the features selected in the main page |
| RetrieveTCGADatasets.php | Retrieve the samples from TCGA, according to the features selected in the main page |
| RetrieveGeneList.php | Retrieve list of genes specific for each dataset (TCGA, CCLE, data returned) for the autocomplete search fields |
| conn_details.php | Page with all the connection (db) details. This page was planned to be encrypted at the final stage of production |
| vars.php | All the variables and useful function to be imported in each script |
| File name | Description |
|---|---|
| candlestick.js | Plugin for interactive buttons |
| ccle.js | Methods for the analysed results of CCLE data |
| tcga.js | Methods for the analysed results of TCGA data |
| data_return.js | Methods for the analysed results of returned data |
| sf.js | Methods for animations and functions in the main webpage |
| network.js | Methods for visualising protein-protein interaction networks |
| jquery.scrollintoView.js | Auto scrolling once the plot is loaded |
| jquery.dataTables.yadcf.js | Look here for further details |
| File name | Description |
|---|---|
| candlestick.css | Plugin for interactive buttons |
| sf.css | Style for elements of the main web page |
| tcga.css | Style for the page collecting analysed results of TCGA data |
| dr.css | Style for the page collecting analysed results of returned data |
| odometer-theme-train-station.css | Style for samples interactive, counter |
R scripts were developed for performing bioinformatics analysis on microarrays, RNA-seq and WGS data. For further details on the available analyses, please refer to our latest publication
| File name | Description |
|---|---|
| CreateExprMatrix.R | Extracts the expression values for selected samples from TCGA or CCLE |
| CreateMutMatrix.R | Extracts mutation values for selected samples (if available) |
| LiveCNAlterations.R | Evaluates copy number alterations for selected genes and plot the results as an interactive heatmap |
| LiveCoExpression.R | Calculates the coexpression between user-defined genes/probes, for selected samples |
| LiveExprCN.R | Visualise copy number alterations (boxplots and barplots) across selected samples |
| LiveExprCNMut.R | Visualise copy number alterations across selected samples. It also integrates mutation profiles |
| LiveGeneExpression.R | Visualise gene expression levels for selected genes |
| LiveMuts.R | Visualise the mutation profile for TCGA data |
| LiveNetworkCreator.R | Visualise an interactive protein interaction network where nodes (genes) are colored according to the expression level in selected samples (average) |
| LiveOncoprint.R | Visualise the mutation profile (oncoprint) for selected genes, across multiple samples |
| LiveSurvivalGene.R | Visualise survival data (for SELECTED genes) as a KM plot. It also produce a JSON file to be imported as an interactive table |
| PCA.R | Performs PCA analysis using normalised expression data on selected samples. It visualise results as an interactive 3D scatterplot |
| Survival.R | Visualise survival data (for ALL genes across selected samples) as a KM plot |
| estimate.R | Evaluates tumour purity of selected samples |
| mclust.R | Identifies triple negative samples. It also assigns Er, PR and Her2 status according to the expression profile |
| pam50.R | Predicts PAM50 breast cancer molecular subtypes and visualise the aboundance as a barplot |
These files contain dictionary for ID conversions, raw data from TCGA or CCLE, sources for conducting pam50 and gene network analyses
| File name | Description |
|---|---|
| SF2BiomartMapping.txt | Link between BCNTB literature service (Biomart) URLs and selectable feautures |
| ccle_cn.csv | Copy number data from Cancer Cell Line Encyclopedia |
| ccle_cn_target_with_chr.csv | Copy number data from Cancer Cell Line Encyclopedia (with chromosome info) |
| ccle_gea_target.txt | Clinical informations for CCLE samples |
| ccle_gene_exp.csv | Gene expression matrix for CCLE sample |
| ccle_gene_list.txt | List of unique genes listed in the "cle_gene_exp.csv" file |
| ccle_mut.csv | Mutations data from Cancer Cell Line Encyclopedia |
| dr_gea_target.txt | Clinical informations for "BCN returned" samples |
| dr_gene_exp.csv | Gene expression matrix for "BCN returned" samples |
| dr_gene_list.txt | List of unique genes listed in the "dr_gene_exp.csv" file |
| dr_mut_exp.txt | Mutations data for "BCN returned" samples |
| dr_gene_list_mut.txt | List of unique genes listed in the "dr_mut_exp.txt" file |
| dr_mut_target.txt | Clinical informations for "BCN returned" samples (where mutation data are available) |
| mentha.txt | Protein-protein interaction data extracted from Mentha database |
| pam50.genes.txt | List of genes to be considered in the PAM50 analysis |
| tcga_gea_target.txt | Clinical informations for TCGA samples |
| tcga_gene_exp.csv | Gene expression matrix for CCLE sample |
| tcga_gene_list.txt | List of unique genes listed in the "tcga_gene_exp.csv" file |
The queries folder contains a tracklog of all the queries launched on the web portal. This represent a useful tool for creating access statistics and other analyses.