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The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

Andrew D. Rouillard, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang, Caroline D. Monteiro, Michael G. McDermott, Avi Ma'ayan
2016 Database: The Journal of Biological Databases and Curation  
Acknowledgements We would like to thank Dr Kathleen Jagodnik for copyediting this article. Conflict of interest. None declared.  ...  Other resources use text-mining strategies to collect information about genes and proteins.  ...  The harmonizome mobile app The Harmonizome mobile application serves the biological knowledge we collected in an easy-to-access interface where a user can enter a gene of interest to discover properties  ... 
doi:10.1093/database/baw100 pmid:27374120 pmcid:PMC4930834 fatcat:ad5eckxnzvczfg2pyhzjlp4amm

Appyters: turning Jupyter Notebooks into data-driven web apps

Daniel J.B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman (+12 others)
2021 Patterns  
Appyters present to users an entry form enabling them to upload their data and set various parameters for a multitude of data analysis workflows.  ...  Jupyter Notebooks have transformed the communication of data analysis pipelines by facilitating a modular structure that brings together code, markdown text, and interactive visualizations.  ...  ACKNOWLEDGMENTS This work was partially supported by NIH grants U24CA224260, U54HL127624, and OT2OD030160.  ... 
doi:10.1016/j.patter.2021.100213 pmid:33748796 pmcid:PMC7961182 fatcat:n2xqpmun45dddfqn756hagj72m

Biomedical Informatics on the Cloud

Peipei Ping, Henning Hermjakob, Jennifer S. Polson, Panagiotis V. Benos, Wei Wang
2018 Circulation Research  
In the digital age of cardiovascular medicine, the rate of biomedical discovery can be greatly accelerated by the guidance and resources required to unearth potential collections of knowledge.  ...  A unified computational platform leverages metadata to not only provide direction but also empower researchers to mine a wealth of biomedical information and forge novel mechanistic insights.  ...  Ding Wang and Bilal Mirza, as well as Anders Garlid, Chelsea Ju, Jessica Lee, Zeyu Li, Patrick Tan, and Justin Wood at the University of California, Los Angeles (UCLA) for their critical input on the content  ... 
doi:10.1161/circresaha.117.310967 pmid:29700073 pmcid:PMC6192708 fatcat:kekqc3gegvcc3hm56xzw3cosmu

"Omics" data integration and functional analyses link Enoyl-CoA hydratase, short chain 1 to drug refractory dilated cardiomyopathy

Nzali V. Campbell, David A. Weitzenkamp, Ian L. Campbell, Ronald F. Schmidt, Chindo Hicks, Michael J. Morgan, David C. Irwin, John J. Tentler
2018 BMC Medical Genomics  
Large-scale "omics" datasets have not been leveraged and integrated with functional analyses to discover potential drivers of cardiomyopathy. This study addresses the knowledge gap.  ...  Variant replication datasets: n = 128 cases and n = 15 controls. Source of datasets: NCBI Sequence Read Archive.  ...  Funding The design of the study and collection, analysis, and interpretation of data and in writing the manuscript was funded by federal educational loans.  ... 
doi:10.1186/s12920-018-0439-6 pmid:30541556 pmcid:PMC6292014 fatcat:czujf4hfkbgilfqfr3gurnr3u4

ESRRA promotes gastric cancer development by regulating the CDC25C/CDK1/CyclinB1 pathway via DSN1

Feng-Nan Li, Qin-Yi Zhang, Ou Li, Shi-Lei Liu, Zi-Yi Yang, Li-Jia Pan, Cheng Zhao, Wei Gong, Yi-Jun Shu, Ping Dong
2021 International Journal of Biological Sciences  
Methods: Kaplan-Meier plot was utilized to find the relationship between ESRRA expression and patients' prognoses. The expression level of ESRRA was measured by real-time PCR.  ...  The protein expression levels were tested with western-blot and immunohistochemistry. Cell cycle and apoptosis was identified with flow cytometry.  ...  Acknowledgements We would like to express gratitude to Laboratory of General Surgery and Department of General Surgery, Xinhua Hospital affiliated with Shanghai Jiao Tong University School of Medicine  ... 
doi:10.7150/ijbs.57623 pmid:34131395 pmcid:PMC8193261 fatcat:ud733gfi6zaapk5iegn3prdo34

HAT cofactor TRRAP modulates microtubule dynamics via SP1 signaling to prevent neurodegeneration

Alicia Tapias, David Lázaro, Bo-Kun Yin, Seyed Mohammad Mahdi Rasa, Anna Krepelova, Erika Kelmer Sacramento, Paulius Grigaravicius, Philipp Koch, Joanna Kirkpatrick, Alessandro Ori, Francesco Neri, Zhao-Qi Wang
2021 eLife  
TRRAP is required for SP1 binding at the promoter proximity of target genes, especially microtubule dynamics.  ...  The ectopic expression of Stathmin3/4 ameliorates defects of TRRAP-deficient neurons, indicating that the microtubule dynamics is particularly vulnerable to the action of SP1 activity.  ...  ., and Ma'ayan, A. (2016). The harmonizome: a collection of processed datasets gathered to 863 serve and mine knowledge about genes and proteins. Database (Oxford) 2016. 864 40.  ... 
doi:10.7554/elife.61531 pmid:33594975 pmcid:PMC7939550 fatcat:yzgont6cnzgaxiwks4slhgbahy

Nubp2 is required for cranial neural crest survival in the mouse [article]

Andrew DiStasio, David Paulding, Praneet Chatuverdi, Rolf W Stottmann
2019 bioRxiv   pre-print
We used exome sequencing to discover a missense mutation in Nucleotide Binding Protein 2 (Nubp2) to be causative.  ...  The N-ethyl-N-nitrosourea (ENU) forward genetic screen is a useful tool for the unbiased discovery of novel mechanisms regulating developmental processes.  ...  https://doi.org/10.1101/656652 doi: bioRxiv preprint Rouillard, A.D., et al., The harmonizome: a collection of processed datasets gathered to serve and 521 mine knowledge about genes and proteins  ... 
doi:10.1101/656652 fatcat:mjrb6v4w6felhnvs3vfgfihuby

Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome [article]

Sara Lago, Filippo M. Cernilogar, Maryam Kazerani, Helena Dominiguez Moreno, Matteo Nadai, Gunnar Schotta, Sara N. Richter
2020 bioRxiv   pre-print
Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different  ...  Cell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization.  ...  The harmonizome: a collection of processed datasets gathered to serve and BG4-encoding plasmid (kindly provided by Professor Shankar Balasubramanian, University of Cambridge, UK) was transformed into  ... 
doi:10.1101/2020.08.27.236778 fatcat:gfk5o46x2jfmpjftbau6qyu64a

C6orf203 controls OXPHOS function through modulation of mitochondrial protein biosynthesis [article]

Sara Palacios-Zambrano, Luis Vazquez-Fonseca, Cristina Gonzalez-Paramos, Laura Mamblona, Laura Sanchez-Caballero, Leo G.J. Nijtmans, Rafael Garesse, Miguel Angel Fernandez-Moreno
2019 bioRxiv   pre-print
C6orf203-KO also provoked a depletion of OXPHOS proteins and decreased the activity of the mitochondrial respiratory chain complexes.  ...  Their central function is to produce cellular energy through the OXPHOS system, and functional alterations provoke so-called mitochondrial OXPHOS diseases.  ...  We want to make a special remembrance to Leo Nijtmans, author of this work, a great scientist and a great person that recently passed away. A  ... 
doi:10.1101/704403 fatcat:kthbi6pejrctjn3iyo24266lze

Deep Learning Approach to Genomic Breakage Study from Primary Sequence [article]

Pora Kim, Hua Tan, Jiajia Liu, Megnyuan Yang, Xiaobo Zhou
2021 bioRxiv   pre-print
Among the diverse location of the breakpoints of structural variants, the fusion genes, which have the breakpoints in the gene bodies and typically identified from RNA-seq data, can provide a highlighted  ...  FusionAI leverages the known fusion breakpoints to provide a prediction model of the fusion genes from the primary genomic sequences via deep learning, thereby helping researchers a more accurate selection  ...  EZH2 is known to regulate MXI1 by targeting from the harmonizome, a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (Rouillard et al., 2016) .  ... 
doi:10.1101/2021.06.03.446904 fatcat:6q5bma7nf5dh5c7r2lhmcf7b6e

Enhancing gene set enrichment using networks

Michael Prummer
2019 F1000Research  
Similar to the genes they contain, gene sets are often regulated in a correlative fashion because they share many of their genes or they describe related processes.  ...  Community detection in combination with automatic labeling and the network representation of gene set clusters further constitute an appealing and intuitive visualization of GSA results.  ...  Acknowledgments The author would like to thank all members of NEXUS and in particular Daniel Stekhoven for fruitful discussions as well as Beate Sick (UZH) and Phil Cheng (USZ) for critically reading the  ... 
doi:10.12688/f1000research.17824.2 pmid:30984382 pmcid:PMC6446501 fatcat:sty6a4djfngbni7bogzpogisbi

CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data [article]

Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R Salick, Joe Raymond, Ajamete Kaykas (+2 others)
2019 bioRxiv   pre-print
CellSIUS outperformed existing approaches, enabled the identification of rare cell populations and, in contrast to other methods, simultaneously revealed transcriptomic signatures indicative of the rare  ...  Using a modular workflow and a large dataset with known cell composition, we benchmarked feature selection and clustering methodologies for scRNA-seq data.  ...  Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, et al. 964 The harmonizome: a collection of processed datasets gathered to serve and mine knowledge 965 about genes and proteins  ... 
doi:10.1101/514950 fatcat:7l5gskahqrdqve6asy3spwikom

GSTM3 Function and Polymorphism in Cancer: Emerging but Promising

Shunda Wang, Jinshou Yang, Lei You, Menghua Dai, Yupei Zhao
2020 Cancer Management and Research  
Here, we provide a general introduction to GSTM3 in order to better understand the role of GSTM3 in cancer.  ...  Glutathione S-transferases mu3 (GSTM3), which belongs to a family of xenobiotic detoxifying phase II enzymes, is associated with carcinogen detoxification and the metabolism of exogenous electrophilic  ...  The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database. 2016;2016. 37. Di Lollo V, Canciello A, Orsini M, et al.  ... 
doi:10.2147/cmar.s272467 pmid:33116892 pmcid:PMC7585806 fatcat:sxvscsowsba77ag6u6vx6znqmu

The structural basis for regulation of the nucleo-cytoplasmic distribution of Bag6 by TRC35 [article]

Jee-Young Mock, Yue Xu, Yihong Ye, William Clemons
2017 bioRxiv   pre-print
The results provide a mechanism for regulation of Bag6 nuclear localization and the functional integrity of the Bag6 complex in the cytosol.  ...  Remarkably, while TRC35 and its fungal homolog guided entry of tail-anchored protein 4 (Get4) utilize a conserved hydrophobic patch to bind their respective C-terminal binding partners Bag6 and Get5, Bag6  ...  We thank members of the laboratory for support and useful discussions. We are grateful to Gordon and Betty Moore for support of the Molecular Observatory at Caltech.  ... 
doi:10.1101/154351 fatcat:4cya4a5gfzggdp7x6vbkqwqztm

Adopting tipping-point theory to transcriptome profiles unravels disease regulatory trajectory [article]

Xinan H Yang, Zhezhen Wang, Dannie Griggs, Qier An, Fangming Tang, John M Cunningham
2019 bioRxiv   pre-print
Applying NPS to neuroblastoma transcriptome of two patient populations yielded two CTSs that reproducibly identified a critical system transition between the low-risk and a high-risk state.  ...  transition signal (CTS) based on coherent expression of genes and lncRNAs shows prognostic significanceGWAS-scans with the CTS unveiled five overlooked genes and four lncRNAs with promising clinical implicationsWe  ...  Bioinformatics 26: 139-40 Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A (2016) The harmonizome: a collection of processed datasets gathered to serve and mine knowledge  ... 
doi:10.1101/668442 fatcat:o7i6obveh5chtm5rcti2hwvmmi
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