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dbDEPC: a database of Differentially Expressed Proteins in human Cancers

Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie, Yixue Li
2009 Nucleic Acids Research  
Here we present a database of differentially expressed proteins in human cancers (dbDEPC), with the goal of collecting curated cancer proteomics data, providing a resource for information on protein-level  ...  dbDEPC is expected to be a reference database for cancer signatures at the protein level.  ...  ACKNOWLEDGEMENT The authors acknowledge Lynne Berry from the Vanderbilt Cancer Biostatistics Center for her editing work.  ... 
doi:10.1093/nar/gkp933 pmid:19900968 pmcid:PMC2808941 fatcat:hnppd37igbbtpgubmc6ky3rtb4

dbDEPC 2.0: updated database of differentially expressed proteins in human cancers

Ying He, Menghuan Zhang, Yuanhu Ju, Zhonghao Yu, Daqing Lv, Han Sun, Weilan Yuan, Fei He, Jianshe Zhang, Hong Li, Jing Li, Rui Wang-Sattler (+3 others)
2011 Nucleic Acids Research  
In 2009, we published the first database of DEPs in human cancers (dbDEPCs).  ...  A large amount of differentially expressed proteins (DEPs) have been identified in various cancer proteomics experiments, curation and annotation of these proteins are important in deciphering their roles  ...  ACKNOWLEDGEMENTS The authors acknowledge the Shanghai Guidance of Science and Technology for the offer of abstracts and full texts of publications collected in dbDEPC.  ... 
doi:10.1093/nar/gkr936 pmid:22096234 pmcid:PMC3245147 fatcat:xsnz7hhkgvcmjm5itjmixdi4y4

dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication

Qingmin Yang, Yuqi Zhang, Hui Cui, Lanming Chen, Yong Zhao, Yong Lin, Menghuan Zhang, Lu Xie
2018 Database: The Journal of Biological Databases and Curation  
., Cui,H. et al. dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication.  ...  Abstract Proteins are major effectors of biological functions, and differentially expressed proteins (DEPs) are widely reported as biomarkers in pathological mechanism, prognosis prediction as well as  ...  , differentially expressed and fold change), restriction of species (human cancer).  ... 
doi:10.1093/database/bay015 pmid:29688359 pmcid:PMC5824774 fatcat:77wqcpl3irbjrg56ga3d64oviq

Human cancer databases (Review)

2014 Oncology Reports  
cancer is one of the four major non-communicable diseases (ncD), responsible for ~14.6% of all human deaths. currently, there are >100 different known types of cancer and >500 genes involved in cancer.  ...  As a result, there is an exponential growth of cancer-associated data from diverse resources, such as scientific publications, genome-wide association studies, gene expression experiments, gene-gene or  ...  Differentially expressed proteins (Deps) that contribute to the onset and progression of cancer have been identified. the first database of Deps in human cancers, dbDepc (57, 58) , currently contains  ... 
doi:10.3892/or.2014.3579 pmid:25369839 pmcid:PMC4254674 fatcat:rqs4fdfqsze4fmypfkbqy4ibzu

Novel bioinformatic identification of differentially expressed tissue-specific and cancer-related proteins from the Human Protein Atlas for biomarker discovery

X.-X. Liu, F.-J. Liu
2015 Genetics and Molecular Research  
The final results included identification of tissue-specific proteins and differentially expressed proteins in different cancer types that are primarily involved in energy metabolism and cell invasion.  ...  Here we performed a new strategy to identify candidate cancer proteins by mining immunohistochemistry protein profiles.  ...  ACKNOWLEDGMENTS Research supported by grants from the National Natural Science Foundation of China (#81300533) and the Shandong Provincial Natural Science Foundation, China (#ZR2013HQ002).  ... 
doi:10.4238/2015.may.4.14 pmid:25966229 fatcat:f27eb5rp3bf4tjuq7hjcfjdw2y

Differential proteomic analysis of pathway biomarkers in human breast cancer by integrated bioinformatics

2012 Oncology Letters  
An integrated bioinformatics analysis of differentially expressed proteins in human breast cancer was performed.  ...  Breast cancer protein profiles were constructed by data mining proteins in literature and public databases, including 1031 proteins with 153 secretory and 69 cell surface proteins.  ...  Differential serum proteomics between human breast cancer patients and healthy volunteers were performed, and western blotting was used to validate the differential expression of secretory proteins in  ... 
doi:10.3892/ol.2012.881 pmid:23162659 pmcid:PMC3499542 fatcat:k7xpe6ialbgt7omqmmpfzrhc5i

SyStemCell: A Database Populated with Multiple Levels of Experimental Data from Stem Cell Differentiation Research

Jian Yu, Xiaobin Xing, Lingyao Zeng, Jiehuan Sun, Wei Li, Han Sun, Ying He, Jing Li, Guoqing Zhang, Chuan Wang, Yixue Li, Lu Xie (+1 others)
2012 PLoS ONE  
Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple  ...  Elucidation of the mechanisms of stem cell differentiation is of great scientific interest.  ...  / biosystems). dbDEPC is an in-house database of differentially expressed proteins in human cancers, which might allow a quick check of tumor relevance for genes identified in stem cell research.  ... 
doi:10.1371/journal.pone.0035230 pmid:22807998 pmcid:PMC3396617 fatcat:7e5lrsailffcdodki4ezwdn3em

Liverome: a curated database of liver cancer-related gene signatures with self-contained context information

Langho Lee, Kai Wang, Gang Li, Zhi Xie, Yuli Wang, Jiangchun Xu, Shaoxian Sun, David Pocalyko, Jong Bhak, Chulhong Kim, Kee-Ho Lee, Ye Jang (+3 others)
2011 BMC Genomics  
A database of the published HCC gene signatures would be useful to liver cancer researchers seeking to retrieve existing differential expression information on a candidate gene and to make comparisons  ...  A number of molecular profiling studies have investigated the changes in gene and protein expression that are associated with various clinicopathological characteristics of HCC and generated a wealth of  ...  Acknowledgements This work was supported in part by the KRIBB  ... 
doi:10.1186/1471-2164-12-s3-s3 pmid:22369201 pmcid:PMC3333186 fatcat:v4yxhdz2ebcp3i4efzlzbeqyre

Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer

J.-H. Lee, S. You, D. Y. Hyeon, B. Kang, H. Kim, K. M. Park, B. Han, D. Hwang, S. Kim
2015 Database: The Journal of Biological Databases and Curation  
Here, we developed an Integrated Database for ARSs (IDA), a resource database including cancer genomic/proteomic and interaction data of ARS/ AIMPs.  ...  IDA includes mRNA expression, somatic mutation, copy number variation and phosphorylation data of ARS/AIMPs and their interacting proteins in various cancers.  ...  Gene expression and protein-interaction data are stored in a MySQL database.  ... 
doi:10.1093/database/bav022 pmid:25824651 pmcid:PMC4377328 fatcat:dj7kn6bqgfbureb5ohe7p42ziu

Web Resources for Stem Cell Research

Ting Wei, Xing Peng, Lili Ye, Jiajia Wang, Fuhai Song, Zhouxian Bai, Guangchun Han, Fengmin Ji, Hongxing Lei
2015 Genomics, Proteomics & Bioinformatics  
In this short review, we have presented a brief overview on major web resources relevant to stem cell research.  ...  To facilitate more efficient use of these resources, we have provided a preliminary rating based on our own user experience of the overall quality for each resource.  ...  Annotations include information from gene ontology (GO), BioCarta, the NCBI BioSystems database, and the database of Differentially Expressed Proteins in human Cancer (dbDEPC).  ... 
doi:10.1016/j.gpb.2015.01.001 pmid:25701763 pmcid:PMC4411488 fatcat:jtldm7fh3vh7hi56hcoihm6yiq

FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets

Evgeny S. Tiys, Timofey V. Ivanisenko, Pavel S. Demenkov, Vladimir A. Ivanisenko
2018 BMC Genomics  
However, existing methods, including CrossTalkZ, do not take into account individual types of interactions, such as protein/protein interactions, expression regulation, transport regulation, catalytic  ...  Using examples of thyroid cancer and apoptosis networks, we have shown that the links over-represented in the analyzed network in comparison with the random ones make possible a biological interpretation  ...  of the number of networks different by at least one type Table 2 2 Enrichment by various types of functional interactions in groups of differentially expressed proteins in thyroid cancer (dbDEPC)  ... 
doi:10.1186/s12864-018-4474-7 pmid:29504895 pmcid:PMC5836822 fatcat:lc4fptk2kbfuzhz3cyyxd2v4mi

An Insight into the Proteome of Uveal Melanoma-Derived Ectosomes Reveals the Presence of Potentially Useful Biomarkers

Surman, Hoja-Łukowicz, Szwed, Kędracka-Krok, Jankowska, Kurtyka, Drożdż, Lityńska, Stępień, Przybyło
2019 International Journal of Molecular Sciences  
The present study investigated the protein content and glycosylation pattern of ectosomes released in vitro by a human primary uveal melanoma Mel202 cell line.  ...  As many as 2527 unique proteins were identified, and many of them are known to be involved in cancer cell proliferation and altered metabolism, tumor invasion, metastasis, or drug resistance.  ...  The dbDEPC 3.0 database (designed to store and display proteins differentially expressed in cancer) was used to select cancer-related proteins and then classify them according to their role in tumor progression  ... 
doi:10.3390/ijms20153789 pmid:31382537 pmcid:PMC6695883 fatcat:mvzick4j3vgz7cs2r4lbzwj55q

Resistance to anticancer vaccination effect is controlled by a cancer cell-autonomous phenotype that disrupts immunogenic phagocytic removal

Abhishek D. Garg, Sanne Elsen, Dmitri V. Krysko, Peter Vandenabeele, Peter de Witte, Patrizia Agostinis
2015 OncoTarget  
Defective ecto-CRT in response to ICD induction was a result of low endogenous CRT protein levels (i.e. CRT lowphenotype) in AY27 cells.  ...  Moreover, we found that a subset of cancer patients of various cancer-types indeed possessed CALR low or CRT low -tumours.  ...  Michael Rory Daws (University of Oslo, Norway) for the RMW phagocytes and Dr. Jakub Golab (Medical University of Warsaw) for the J774 phagocytes.  ... 
doi:10.18632/oncotarget.4754 pmid:26314964 pmcid:PMC4694957 fatcat:iqzmbq3x5vevbavgp6yrx3dwtq

Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery

Yang Woo Kwon, Han-Seul Jo, Sungwon Bae, Youngsuk Seo, Parkyong Song, Minseok Song, Jong Hyuk Yoon
2021 Frontiers in Medicine  
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins.  ...  In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage.  ... cmpd dbDEPc 3.0 -26 cancer types (28 subtypes) -Proteomics Database of differentially expressed proteins in cancers with multi-level annotations and drug indications.  ... 
doi:10.3389/fmed.2021.747333 pmid:34631760 pmcid:PMC8492935 fatcat:iootztqtqncxnchjpyhh5ewkee

Big data: the next frontier for innovation in therapeutics and healthcare

Naiem T Issa, Stephen W Byers, Sivanesan Dakshanamurthy
2014 Expert Review of Clinical Pharmacology  
We are in the era of the '-omics', wherein an individual's genome, transcriptome, proteome and metabolome can be scrutinized to the finest resolution to paint a personalized biochemical fingerprint that  ...  While individualized patient management is a key beneficiary of next-generation medical informatics, this data also harbors a wealth of novel therapeutic discoveries waiting to be uncovered.  ...  PRIDE The Human Protein Atlas UniProt Database of differentially expressed proteins in human cancer Clinical and cell line protein LC-MS/MS and 2D-difference gel electrophoresis for expression  ... 
doi:10.1586/17512433.2014.905201 pmid:24702684 pmcid:PMC4448933 fatcat:77p3ulhl3rfm3ktapyepnqeelu
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