Abstract
Autophagy is an essential cellular process that is closely implicated in diverse pathophysiological processes and a variety of human diseases, especially tumors. Autophagy is regarded as not only an anti-cancer process in tumorigenesis but also a pro-tumor process in progression and metastasis according to current research. It means the role of autophagy in tumor is considered to be complex, controversial and context dependent. Hence, a comprehensive database is of great significance to obtain an in-depth understanding of such complex correlations between autophagy and tumor. To achieve this objective, here we developed the Autophagy and Tumor Database (named as ATdb, http://www.bigzju.com/ATdb/#/) to compile the published information concerning autophagy and tumor research. ATdb connected 25 types of tumors with 137 genes required for autophagy-related pathways, containing 219 population filters, 2650 hazard ratio trend plots, 658 interacting microRNAs, 266 interacting long non-coding RNAs, 155 post-translational modifications, 298 DNA methylation records, 331 animal models and 70 clinical trials. ATdb could enable users to search, browse, download and carry out efficient online analysis. For instance, users can make prediction of autophagy gene regulators in a context-dependent manner and in a precise subpopulation and tumor subtypes. Also, it is feasible in ATdb to cluster tumors into distinguished groups based on the gene-related long non-coding RNAs to gain novel insights into their potential functional implications. Thus, ATdb offers a powerful online database for the autophagy community to explore the complex world of autophagy and tumor.Database URL: http://www.bigzju.com/ATdb/#/
Highlights
As a highly conserved cellular process, macroautophagy is essential for the degradation of cytoplasmic components to recycle intracellular substances so as to maintain the cellular homeostasis [1,2,3,4,5]
The clinical effects of autophagy were analyzed in 25 types of tumors with data from The Cancer Genome Atlas (TCGA) and 93 Gene Expression Omnibus data sets
To elucidate autophagy-mediated metastasis in a contextdependent nature, mechanisms and context underlying the role of autophagy in metastasis were reviewed by Dower et al [20]
Summary
As a highly conserved cellular process, macroautophagy (hereafter referred to as autophagy) is essential for the degradation of cytoplasmic components to recycle intracellular substances so as to maintain the cellular homeostasis [1,2,3,4,5]. Great advances have been made in deciphering the molecular mechanisms of autophagy, as well as in understanding the pathophysiological effects of abnormal autophagy in disease conditions such as tumor [2, 6, 7]. [1, 2] Both the core ATG proteins and their regulators are functionally modulated by various mechanisms, such as transcriptional regulation, post-translational modification (PTM), protein–protein interaction, non-coding RNA and chemical/pharmacological compounds [8,9,10,11]. Another aspect of challenge comes from its complex effects on disease especially on tumor. Capture, compiling, annotation and analysis of such information are of great significance
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