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BioGPS: building your own mash-up of gene annotations and expression profiles

Chunlei Wu, Xuefeng Jin, Ginger Tsueng, Cyrus Afrasiabi, Andrew I. Su
2015 Nucleic Acids Research  
The unique features of BioGPS, compared to those of other gene portals, are its community extensibility and user customizability.  ...  BioGPS (http://biogps.org) is a centralized geneannotation portal that enables researchers to access distributed gene annotation resources.  ...  ACKNOWLEDGEMENTS The authors acknowledge contributions, comments and suggestions from the BioGPS user community.  ... 
doi:10.1093/nar/gkv1104 pmid:26578587 pmcid:PMC4702805 fatcat:jru2uucc7bbnzidmolxuyp4vbu

Review of Machine Learning Applications and Datasets in Classification of Acute Leukemia

Jaishree Ranganathan
2021 International Journal of Data Mining & Knowledge Management Process  
Leukemia is a cancer of the white blood cells and some other cell types. Diagnosing leukemia is laborious in a multitude of areas including heamatology.  ...  In addition to describing the existing literature, this work aims to identify different sources of publicly available data that could be utilised for research and development of intelligent machine learning  ...  Afrasiabi, and A. I. Su, “Biogps: building your own mash-up of gene annotations and expression profiles,” Nucleic acids research, vol. 44, no. D1, pp. D313–D316, 2016. [34] M. Mohamed, B.  ... 
doi:10.5121/ijdkp2021.11601 fatcat:y2yoy443czd5bgday3r6q4i7h4

A High Resolution Atlas Of Gene Expression In The Domestic Sheep (Ovis aries) [article]

Emily L. Clark, Stephen J. Bush, Mary E. B. McCulloch, Iseabail L. Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu-Gwen Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, Bruce Whitelaw (+4 others)
2017 bioRxiv   pre-print
Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes.  ...  The principle of guilt by association was used to infer the function of uncharacterised genes from their co-expression with genes of known function.  ...  Tissue-based map of the human proteome. Science. 2015;347(6220). doi: Jin X, Tsueng G, Afrasiabi C, Su AI. BioGPS: building your own mash-up of gene annotations and expression profiles.  ... 
doi:10.1101/132696 fatcat:5jgki36dlndhlisaeubo33vx6y

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Oscar D. Murillo, William Thistlethwaite, Joel Rozowsky, Sai Lakshmi Subramanian, Rocco Lucero, Neethu Shah, Andrew R. Jackson, Srimeenakshi Srinivasan, Allen Chung, Clara D. Laurent, Robert R. Kitchen, Timur Galeev (+46 others)
2019 Cell  
The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools.  ...  Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers.  ...  ., and Su, A.I. (2016). BioGPS: building your own mash-up of gene annotations and expression profiles. Nucleic Acids Res. 44 (D1), D313-D316.  ... 
doi:10.1016/j.cell.2019.02.018 pmid:30951672 pmcid:PMC6616370 fatcat:b4sgq7q2bvhi7lu22tspmpviiu

mEAK-7 Forms an Alternative mTOR Complex with DNA-PKcs in Human Cancer

Joe Truong Nguyen, Fatima Sarah Haidar, Alexandra Lucienne Fox, Connor Ray, Daniela Baccelli Mendonça, Jin Koo Kim, Paul H. Krebsbach
2019 iScience  
We demonstrate that mEAK-7 and mTOR signaling are strongly elevated in tumor and metastatic lymph nodes of patients with non-small-cell lung carcinoma compared with those of patients with normal lung or  ...  DNA-PKcs pharmacologic inhibition or genetic knockout reduced S6K2, mEAK-7, and mTOR binding with DNA-PKcs, resulting in loss of S6K2 activity and mTOR signaling.  ...  BioGPS: building your own mash-up of gene annotations and expression profiles. Nucleic Acids Res. 44, D313-D316. Wu, C., Macleod, I., and Su, A.I. (2013).  ... 
doi:10.1016/j.isci.2019.06.029 pmid:31288154 pmcid:PMC6614755 fatcat:qdz32rpb3rhndkbqmbkoyqzayu

Temporal epigenomic profiling identifies AHR and GLIS1 as super-enhancer controlled regulators of mesenchymal multipotency [article]

Deborah Gerard, Florian Schmidt, Aurelien Ginolhac, Martine Schmitz, Rashi Halder, Peter Ebert, Marcel H. Schulz, Thomas Sauter, Lasse Sinkkonen
2017 bioRxiv   pre-print
Temporal data on gene expression and context-specific open chromatin states can improve identification of key transcription factors (TFs) and the gene regulatory networks (GRNs) controlling cellular differentiation  ...  To prioritize the identified shared regulators, we mapped dynamic super-enhancers in both lineages and associated them to target genes with correlated expression profiles.  ...  BioGPS: building your 12 own mash-up of gene annotations and expression profiles. Nucleic Acids Res, 13 44(D1), D313-316. doi:10.1093/nar/gkv1104 14 Wu, H., Gordon, J. A., Whitfield, T. W., Tai, P.  ... 
doi:10.1101/183988 fatcat:tkq3cfemi5gm5i6r4riefgl4f4

Defining tissue- and disease-associated macrophages using a transcriptome-based classification model [article]

Hung-Jen Chen, Andrew Y.F. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
2019 bioRxiv   pre-print
Here, we aggregated public expression data to define consensus expression profiles for eight commonly-used in vitro macrophage models.  ...  This classifier was subsequently applied to transcriptional profiles of tissue-isolated and disease-associated macrophages to specifically define macrophage characteristics in vivo.  ...  Su, BioGPS: building your own mash-up of gene 475annotations and expression profiles. Nucleic Acids Res 44, D313-316 (2016).All rights reserved. No reuse allowed without permission. 30. P. G.  ... 
doi:10.1101/532986 fatcat:4zm2jrpuqbaodo3knaokkz2ciu

Baseline pulmonary levels of CD8+ T cells and NK cells inversely correlate with expression of the SARS-CoV-2 entry receptor ACE2 [article]

Pascal H. G. Duijf
2020 biorxiv/medrxiv  
Baseline levels of CD8+ T cells, resting natural killer (NK) cells and activated NK cells are significantly lower in lung tissues with high expression of the SARS-CoV-2 host cell entry receptor ACE2.  ...  Thus, our results suggest that a subgroup of individuals may be exceedingly susceptible to COVID-19 due to concomitant high pre-existing ACE2 expression and low baseline cytotoxic lymphocyte levels in  ...  A human homolog of Wu C, Jin X, Tsueng G, Afrasiabi C, Su AI. 2016. BioGPS: building your own mash-up of gene //doi.org/10.1093/nar/gkv1104. 59.  ... 
doi:10.1101/2020.05.04.075291 pmid:32511391 pmcid:PMC7263520 fatcat:u242ui45q5eynmolmupileviry

Making sense of the cause of Crohn's – a new look at an old disease

Anthony W. Segal
2016 F1000Research  
Wu C, Jin X, Tsueng G, et al.: BioGPS: building your own mash-up of gene annotations and expression profiles. Nucleic Acids Res. 2016; 44(D1): D313-6.  ...  Holgersen K, Kutlu B, Fox B, et al.: High-resolution gene expression profiling using RNA sequencing in patients with inflammatory bowel disease and in mouse models of colitis.  ...  Acknowledgements I thank Holm Ulhig and Amnon Sonnenberg for permission to publish figures from their papers. I am indebted to Adam Levine for assistance with the preparation of this manuscript.  ... 
doi:10.12688/f1000research.9699.1 pmid:28105308 pmcid:PMC5224693 fatcat:j7yvzk4jxne25jlfxdaigegcba