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BioGPS: building your own mash-up of gene annotations and expression profiles
2015
Nucleic Acids Research
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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
2021
International Journal of Data Mining & Knowledge Management Process
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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]
2017
bioRxiv
pre-print
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2019
Cell
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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
2019
iScience
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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]
2017
bioRxiv
pre-print
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The file type is application/pdf.
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]
2019
bioRxiv
pre-print
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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]
2020
biorxiv/medrxiv
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The file type is application/pdf.
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
2016
F1000Research
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The file type is application/pdf.
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