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Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues

Nicole Zatorski, David Stein, Rayees Rahman, Ravi Iyengar, Avner Schlessinger
2022 Database: The Journal of Biological Databases and Curation  
We have developed structural signatures, a web server for annotating and analyzing protein features from gene sets that are often found in transcriptomic and proteomic data.  ...  This platform provides access to a structural feature database derived from normal and disease human tissue samples.  ...  Database Explorer page The server also allows users to explore the structural features of normal human tissue samples in the GTEx (7) and ARCHS4 ( 8 ) databases (Figure 3 ).  ... 
doi:10.1093/database/baac053 pmid:35881481 pmcid:PMC9319604 fatcat:c6s36dg4bvbnfgpmvtncrkku6y

Protein structural consequences of DNA mutational signatures: A meta-analysis of somatic variants and deep mutational scanning data [article]

Joseph Chi-Fung Ng, Franca Fraternali
2021 bioRxiv   pre-print
cell, particularly the distribution of the resulting variants in the implied proteins and their structural regions (surface, core, interacting interface).  ...  Here we first compare the protein-level consequences of six mutational signatures (Aging, APOBEC, POLE, UV, 5-FU and Platinum) characterised by clear DNA motif preferences.  ...  For cell lines where multiple vcfs were available, 342 data generated from Illumina HiSeq 2000 was taken.  ... 
doi:10.1101/2021.05.27.445950 fatcat:ocdvfwur6nf2zmqe6ps6zduwsi

Gene Signature-Based Drug Repositioning [chapter]

Zhilong Jia, Xinyu Song, Jinlong Shi, Weidong Wang, Kunlun He
2021 Drug Repurposing - Molecular Aspects and Therapeutic Applications [Working Title]  
of the approved drugs; 4) gene signature databases of various diseases; 5) gene signature-based methods and tools for drug repositioning; 6) new omics technology for drug repositioning; 7) drug repositioning  ...  We will cover the following topics in this chapter. 1) An introduction to the basic discipline of gene signature-based drug repurposing; 2) databases of genes, drugs and diseases; 3) gene signature databases  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China [grant number 31701155].  ... 
doi:10.5772/intechopen.101377 fatcat:s4w2wts33bewfcnnbplvjr5efq

A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes

Bernard Fongang, Fanping Kong, Surendra Negi, Werner Braun, Andrzej Kudlicki
2016 Scientific Reports  
The signature is present in segmented bilaterian animals as evolutionarily distant as humans and flies.  ...  Here, we report the discovery of a conserved feature of the DNA coding for Hox genes and certain other developmental transcription factors.  ...  (UL1TR000071 and UL1TR001439) from the National Center for Advancing Translational Sciences, National Institutes of Health; by March of Dimes grant 5-FY10-136; and by the National Institutes of Health  ... 
doi:10.1038/srep35415 pmid:27739488 pmcid:PMC5064350 fatcat:apotvkiu2vd7lbnrjn5l544eua

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures

2019 Nucleic Acids Research  
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbation-response signatures  ...  of signatures across the entire library independent from the originating source, project or assay.  ...  We acknowledge resources from the Center for Computational Science at the University of Miami for maintaining and administering the production environment and server for the LINCS Data Portal and related  ... 
doi:10.1093/nar/gkz1023 pmid:31701147 pmcid:PMC7145650 fatcat:mx256xxvxrfgzbesb6la2fxqne

Recognition of a Novel Gene Signature for Human Glioblastoma

Chih-Hao Lu, Sung-Tai Wei, Jia-Jun Liu, Yu-Jen Chang, Yu-Feng Lin, Chin-Sheng Yu, Sunny Li-Yun Chang
2022 International Journal of Molecular Sciences  
The identification of a gene signature for GBM may be helpful for its diagnosis, treatment, prediction of prognosis and even the development of treatments.  ...  Protein functional analysis by CELLO2GO implied that these signature genes might be involved in regulating various aspects of biological function, including anatomical structure development, cell proliferation  ...  . , 200) for every 200 generations. Thus, we generated a total of 2000 solutions. After deleting the redundant solutions, the top 10 were obtained from the remainder and ranked by fitness value.  ... 
doi:10.3390/ijms23084157 pmid:35456975 pmcid:PMC9029857 fatcat:diqajtdlnjfgjmahhd7ntd3wxa

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures

2018 Briefings in Bioinformatics  
The contextualization of these patterns is important for obtaining mechanistic insight into the aberrant processes associated with a disease, and this typically involves the integration of multiple heterogeneous  ...  Large amounts of data emerging from experiments in molecular medicine are leading to the identification of molecular signatures associated with disease subtypes.  ...  The work was also partially supported by Core Research for Evolutional Science and Technology (CREST) Grant from the Japan Science and Technology Agency (Grant Number: JPMJCR1412), and Japan Society for  ... 
doi:10.1093/bib/bby025 pmid:29684165 pmcid:PMC6556902 fatcat:iyfard4tdzgnnmhhiqibld756a

TOXsIgN: a cross-species repository for toxicogenomic signatures

Thomas A Darde, Pierre Gaudriault, Rémi Beranger, Clément Lancien, Annaëlle Caillarec-Joly, Olivier Sallou, Nathalie Bonvallot, Cécile Chevrier, Séverine Mazaud-Guittot, Bernard Jégou, Olivier Collin, Emmanuelle Becker (+3 others)
2018 Bioinformatics  
Given the increasing demand for access to this information, we developed TOXsIgN, a repository for TOXicogenomic sIgNatures.  ...  Results: The TOXsIgN repository provides a flexible environment that facilitates online submission, storage, and retrieval of toxicogenomic signatures by the scientific community.  ...  Acknowledgements We thank the GenOuest bioinformatics facility for hosting the software as well as all members of the Research Institute for Environmental and Occupational Health (IRSET) for stimulating  ... 
doi:10.1093/bioinformatics/bty040 pmid:29385404 fatcat:7dnmqxdbizhorkxcwvml4zyv7a

GEN3VA: aggregation and analysis of gene expression signatures from related studies

Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicholas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter Man-Un Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma'ayan
2016 BMC Bioinformatics  
In a second case study, we collected 86 signatures from treatment of human cells with dexamethasone, a glucocorticoid receptor (GR) agonist.  ...  Genome-wide gene expression profiling of mammalian cells is becoming a staple of many published biomedical and biological research studies.  ...  Funding This work is partially supported by the National Institutes of Health (NIH) grants U54HL127624, U54CA189201, and R01GM098316 to AM. Availability of data and materials Not applicable.  ... 
doi:10.1186/s12859-016-1321-1 pmid:27846806 pmcid:PMC5111283 fatcat:vlfpektbkfgtbnds2hafvwqd7a

PharmOmics: A Species- and Tissue-specific Drug Signature Database and Online Tool for Toxicity Prediction and Drug Repurposing [article]

YEN-WEI CHEN, Douglas Arneson, Graciel Diamante, Jennifer Garcia, Nima Zaghari, Paul Patel, Patrick Allard, Xia Yang
2019 bioRxiv   pre-print
Comparison of our PharmOmics platform with other commonly used drug signature databases, most of which are based on data derived from in vitro cell lines, demonstrates that our tissue- and species-specific  ...  Here, we present a comprehensive drug knowledgebase and analytical tool, PharmOmics, comprised of genomic footprints of drugs in individual tissues from multiple species (human, mouse, and rat) based on  ...  Although the tree structure in Brenda 449 Tissue Ontology may assign a cell or tissue to multiple systems (for example, breast cancer 450 cell line may be categorized as both epithelial and breast organ  ... 
doi:10.1101/837773 fatcat:j6eztvgc3bbmhjyhootvh4ayny

Integrated Analyses Identify Immune-Related Signature Associated with Qingyihuaji Formula for Treatment of Pancreatic Ductal Adenocarcinoma Using Network Pharmacology and Weighted Gene Co-Expression Network

Xiang Qian, Zhuo Chen, Sha Sha Chen, Lu Ming Liu, Ai Qin Zhang
2020 Journal of Immunology Research  
The relative expression and methylation levels of OGEs were detected in UALCAN, human protein atlas (HPA), Oncomine, DiseaseMeth version 2.0 and, MEXPRESS database, respectively.  ...  Further, methylation analyses suggested that the abnormal up-regulation of these OGEs probably resulted from hypomethylation, and GSEA revealed the genes markedly related to cell cycle and proliferation  ...  Acknowledgments This study was supported by the National Natural Science Foundation of China (No. 81673742) and the project of Young talents of traditional Chinese Medicine of Zhejiang Provincial (No.  ... 
doi:10.1155/2020/7503605 pmid:32537471 pmcid:PMC7256764 fatcat:nshg4ls3qvhxbd2dszbwhd6v2u

Evolution of the Twist Subfamily Vertebrate Proteins: Discovery of a Signature Motif and Origin of the Twist1 Glycine-Rich Motifs in the Amino-Terminus Disordered Domain

Yacidzohara Rodriguez, Ricardo R. Gonzalez-Mendez, Carmen L. Cadilla, Bin Xue
2016 PLoS ONE  
Disordered domain and secondary structure predictions showed that the amino acid sequence and disorder feature found at the N-terminus is highly evolutionary conserved and could be a functional site that  ...  We identified a new signature motif that is characteristic of each Twist paralog and identified important residues within this motif that can be used to distinguish between these two paralogs, which will  ...  YR received support from a Research Assistantship from the UPR Medical Sciences Campus and NIGMS RISE grant R25GM061838.  ... 
doi:10.1371/journal.pone.0161029 pmid:27556926 pmcid:PMC4996418 fatcat:74dmbr5x5vd4nous66ofwtvsui

A novel cuproptosis-related prognostic lncRNA signature and lncRNA MIR31HG/miR-193a-3p/TNFRSF21 regulatory axis in lung adenocarcinoma

Xiaocong Mo, Di Hu, Pingshan Yang, Yin Li, Shoaib Bashir, Aitao Nai, Feng Ma, Guoxia Jia, Meng Xu
2022 Frontiers in Oncology  
MIR31HG was highly expressed in LUAD specimens and some LUAD cell lines. Inhibition of MIR31HG clearly reduced the proliferation, migration, and invasion of the LUAD cells.  ...  Lung adenocarcinoma (LUAD) remains the most common subtype of lung malignancy. Cuproptosis is a newly identified cell death which could regulate tumor cell proliferation and progression.  ...  Acknowledgments We thank the investigators and patients in the TCGA and GEO for providing data.  ... 
doi:10.3389/fonc.2022.927706 pmid:35936736 pmcid:PMC9353736 fatcat:pal4yhlzjfgqhpntf4gbmc7kbi

Proteins: Sequence to Structure and Function – Current Status

Sandhya R. Shenoy, B. Jayaram
2010 Current protein and peptide science  
In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic change of focus towards sequence analysis has spurred the advent of the genome projects and the resultant diverging  ...  In this article, we attempt to provide a critical assessment of what one may and may not expect from the biological sequences and to identify major issues yet to be resolved.  ...  explored for generating a higher number of clinical drugs [192] .  ... 
doi:10.2174/138920310794109094 pmid:20887265 fatcat:d7jfqzg7lvg5bf3lt4uefm25me

Identification of a Six Gene Prognosis Signature for Papillary Thyroid Cancer Using Multi-Omics Methods and Bioinformatics Analysis

He Ren, Xin Liu, Fuxin Li, Xianghui He, Na Zhao
2021 Frontiers in Oncology  
A protein-protein interaction network was then built and analyzed utilizing STRING and Cytoscape, followed by the identification of 13 hub genes by cytoHubba.  ...  These findings provided new insights into PTC pathogenesis and identified six candidate gene prognosis signature for PTC.  ...  and XL revised the images. HR and FL performed the literature search and data collection. NZ and XH revised the manuscript. All authors contributed to the article and approved the submitted version.  ... 
doi:10.3389/fonc.2021.624421 pmid:33816258 pmcid:PMC8012734 fatcat:zo2tqzekx5cejcj6vdau7dxqwa
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