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Overview
Regulated cell death(RCD) is a ubiquitous process in living organisms that plays a pivotal role in various biological processes, including development, tissue homeostasis, and immune response. Various forms of regulated cell death have been reported to involve in complex cellular process, effecting physiological, or pathological conditions of different tissues. Cumulative evidence supports that regulated cell death isintricately linked to the response and clinical outcomes of different disease treatments. However there is not yet a system-level repository about regulated cell death regulators and its association with various types of diseases. In order to help researchers get know better about mechanism of different regulated cell death and cross-talk between them in different diseases, here we established user-friendly DiseaseCDR website, which contains 18 types of currently known regulated cell death: anoikis, alkaliptosis, apoptosis, autophagy, autosis, cuproptosis, disulfidptosis, entotic_cd, ferroptosis, mpt, immunogenic, lysosomal cell death, mitotic cell death, necroptosis, netotic cell death, oxeiptosis, parthanatos, pyroptosis. For each form of regulated cell death, we collected gene regulator, chemicals regulator and associated diseases from published literature. For gene regulator, the total number of regulator is 18347, include 11754 mRNA, 298 miRNA, and 6295 lncRNA; For chemical regulator, the total number of regulator is 1463, include 504 inducer, 715 inhibitor, and 244 other compunds; For diseases, there were 124 kinds of diseases associated with regulated cell death. Further more DiseaseCDR helps the investigators to acquire transcription factors, miRNAs and signaling pathways implicated in regulated cell death pathway by combing PPI and singlink 3.0. Last of last, DiseaseCDR provide various of analyze tools include diffexp visualization, survival curve, RCD score, RCD score & prognosis, RCD score & Immune infiltration to help researchers` study. We will consistently collect literature data to fullfill our database and maintain the website to fuel regulated cell death research.
1. Overview
1.1 Disease specific cell death gene regulator search
Click "Search", and then 1 choose "Disease types", 2 "Regulated cell death type" step by step. Only you have selected the disease type then the associated regulated cell death type will be list for your choose. 3 Last click "search" button to get the search results.
As the result, DiseaseCDR provide the disease specific regulated cell death gene regulator list. As shown: 1 The selected human disease. 2 The selected regulated cell death type. 3 Further search in search results. 4 Click genesymbol for detai information of the selected gene regulator.
Visualization of Ensemble Learning Classification Model. As shown: 1 The sample distribution dot plot. 2 The ROC curve.
1.2 Quick search
"Quick Search" 1 Click the tissue or txt along. 2 Disease specific regulated cell death gene regulator search. 3 Chemical regulator of regulated cell death search. 4 Regulated cell death associated disease search.
1.3 Gene Detail
As the result, DiseaseCDR provide the disease specific regulated cell death gene regulator list. As shown: 1 The basic information of gene regulator. 2 The description of gene regulator in published literatures. 3 GO annotation. 4 KEGG annotation. 5 Protein-protein interaction network. 6 Gene-drug network. 7 Regulators target to regulated cell death gene regulator. 8 Diff exp and survive visualization of regulated cell death gene regulator.
1.3.1 Visualization.
2. Browse
2.1 Gene Regulator Browse
1 Click "Gene Regulator", and then choose 2 "Gene type", 3 "Regulated cell death type" step by step. Last click "search" button to get the search results. There were four gene types for choose: mRNA, miRNA, lncRNA and pathway. With different selection, the corresponding results will display after 4 click "search" button.
As the result, DiseaseCDR provide the detail information for each gene regulator about the selected gene type and regulated cell death type. As shown: 1 The selected gene type. 2 The selected regulated cell death type. 3 Further search in search results. 4 Click genesymbol for detai information of the selected gene regulator.
2.2 Chemical Regulator Browse
1 Click "Chemical Regulator", and then choose 2 "chemical type", 3 "Regulated cell death type" step by step. Last 4 click "search" button to get the search results. There were three chemical types for choose: inducer, inhibitor and other. With different selection, the corresponding results will display after click "search" button.
As the result, DiseaseCDR provide the published literature for each chemical regulator about the selected chemical type and regulated cell death type. As shown: 1 The selected chemical type. 2 The selected regulated cell death type. 3 Further search in search results.
2.3 Disease Browse
1 Click "Disease", and then choose 2 "Regulated cell death type" step by step. Last 3 click "search" button to get the search results. Simply by click "search" button, the human disease associated with regulated cell death will display.
As the result, DiseaseCDR provide the published literature description for human disease associated with selected regulated cell death type. As shown: 1 The selected regulated cell death type. 2 Further search in search results.
3. Analyze tools Overview
3.1 Regulated cell death score & prognosis
By selecting cancer type and cell death forms users can calculate the regulated cell death score and analyze its association with prognosis in different cancers for their interested cell death form they selected.
As the result, DiseaseCDR provided the calculated RCD score table and the weblink which to download.
Further, the RCD score density and survival curve picture also provided.
3.2 Regulated cell death score immune infiltration
By selecting cancer type, cell death forms and immune infiltration analysis methods users can calculate the regulated cell death score and then luanch the immune infiltration analysis between high and low rcd score group.
As the result, DiseaseCDR provided the immune cell fraction result table and the weblink which to download.
Two immune cell infiltration analyze methods: Epic and xCell were surpported in DiseaseCDR. And the immune cell fraction between high and low RCD score group likes below.
4. Download
DiseaseCDR collected gene(mRNA, miRNA,lncRNA), chemical regulators, pathways and diseases associated with 18 form of regulated cell death. For each type of regulated cell death, users can download the merged file which include all the information just by click the regulated cell death type name in the word cloud. Or click "Download" button after choose data set and regulated cell death type to download corresponding part of the selected regulated cell death type!
1 Click regulated cell death name to download merged file. 2 Choose data set. 3 Choose regulated cell death type. 4 Download selected file.
5. Submission
Submission of any format information about regulated cell death were welcomed. All you need to do is select the file and click submit.
1 Choose file. 2 Submit file.
