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VOLCANO PLOTS IN ANALYZING DIFFERENTIAL EXPRESSIONS WITH mRNA MICROARRAYS

WENTIAN LI
2012 Journal of Bioinformatics and Computational Biology  
This review attempts to provide an unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis  ...  We also discuss the possibility to apply volcano plots to other fields beyond microarray.  ...  Acknowledgements I would like to thank Frank Batliwalla, Percio Gulko, Max Brenner, Peter Gregersen for asking about differences between genes selected by fold-change and those by t-test, which provided  ... 
doi:10.1142/s0219720012310038 pmid:23075208 fatcat:6je75ybe5ndlbpmdrt4hvsaisi

The ketogenic diet reverses gene expression patterns and reduces reactive oxygen species levels when used as an adjuvant therapy for glioma

Phillip Stafford, Mohammed G Abdelwahab, Do Kim, Mark C Preul, Jong M Rho, Adrienne C Scheck
2010 Nutrition & Metabolism  
Methods: Here, we examined the effects of an experimental KD on a mouse model of glioma, and compared patterns of gene expression in tumors vs. normal brain from animals fed either a KD or a standard diet  ...  , especially by inducing glycopenia.  ...  We thank the NIH Neuroscience Microarray consortium for their assistance. This paper is dedicated to the memory of Eleazar Rodriquez.  ... 
doi:10.1186/1743-7075-7-74 pmid:20831808 pmcid:PMC2949862 fatcat:z32iw3heanf7djc46txgyeq6ra

Machine learning analysis using 77,044 genomic and transcriptomic profiles to accurately predict tumor type

Jim Abraham, Amy B. Heimberger, John Marshall, Elisabeth Heath, Joseph Drabick, Anthony Helmstetter, Joanne Xiu, Daniel Magee, Phillip Stafford, Chadi Nabhan, Sourabh Antani, Curtis Johnston (+3 others)
2021 Translational Oncology  
Pathologist evaluation of discrepancies between submitted diagnosis and MI GPSai predictions resulted in change of diagnosis in 41.3% of the time.  ...  MI GPSai provides clinically meaningful information in a large proportion of CUP cases and inclusion of MI GPSai in clinical routine could improve diagnostic fidelity.  ...  Supplementary materials Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.tranon.2021.101016 .  ... 
doi:10.1016/j.tranon.2021.101016 pmid:33465745 pmcid:PMC7815805 fatcat:cijqf4bcyrdgdkclcrm6ma4p5m

Transcriptomic Plasticity in the Arthropod Generalist Tetranychus urticae Upon Long-Term Acclimation to Different Host Plants

Simon Snoeck, Nicky Wybouw, Thomas Van Leeuwen, Wannes Dermauw
2018 G3: Genes, Genomes, Genetics  
KEYWORDS plant defense host plant use xenobiotic metabolism single PLAT domain protein short-chain dehydrogenase Host plant acceptance by a herbivore is influenced by the nutrient composition, with the  ...  In addition to the nutrient composition of a potential host plant, plant defenses play a pivotal role in host plant acceptance.  ...  script for drafting panel B in both Figure 4 LITERATURE CITED  ... 
doi:10.1534/g3.118.200585 fatcat:7kytn6lpizbvhljrxh44o3fiyu

Development, Pathogenesis, and Regeneration of the Intervertebral Disc: Current and Future Insights Spanning Traditional to Omics Methods

Tara T. Hickman, Sudiksha Rathan-Kumar, Sun H. Peck
2022 Frontiers in Cell and Developmental Biology  
Indeed, back pain results in substantial socioeconomic losses and healthcare costs globally each year, with about 85% of the world population experiencing back pain at some point in their lifetimes.  ...  Currently, therapeutic strategies for treating IVD degeneration are limited, and as such, there is great interest in advancing treatments for back pain.  ...  , an activinbinding protein, working in tandem with Noggin (Stafford et al., 2014) .  ... 
doi:10.3389/fcell.2022.841831 pmid:35359439 pmcid:PMC8963184 fatcat:n5t2kfelmnhjvlaobpkwm5mcd4

2012 WVAS abstracts

Joseph Horzempa
2016 Proceedings of the West Virginia Academy of Science  
In order to investigate the p53-pRb crosstalk pathway, an Agilent 44k whole human genome microarray analysis was performed on normal human lung fibroblast cells (WI38) following over-expression of p53,  ...  We have previously shown by microarray analysis that that the gene encoding FGF9 is up-regulated two-fold in meningioma samples versus healthy meninges.  ... 
doi:10.55632/pwvas.v84i1.148 fatcat:fbc3ctpxing3hen2hmjkbrm77q

LC-MS/MS measurement of parathyroid hormone PTH (1-34): Use in studying oral PTH (1-34) administration and possible diagnostic application in pseudohypoparathyroidism

Sulaiman Al-Riyami, Jonathan Tang, Hillel Galitzer, William Fraser
2017 Endocrine Abstracts  
The abstracts submitted were marked by the Abstract Marking panel selected by the Programme Committee.  ...  and World of Science had inaugurated a medical column edited by a member of the London medical establishment.  ...  Methods Formalin-fixed paraffin embedded pancreatic sections from 17 non-diabetic controls, and 6 Type 1 diabetes patients were studied, together with a human tissue microarray.  ... 
doi:10.1530/endoabs.50.p042 fatcat:mlqefg6jxbevjcab3eid4sfxpy

Poster Session I

2014 Neuropsychopharmacology  
The transcripts increased in both FC and AMY are known to be influenced by IFN-a receptor signaling (p ¼ 4.4 x 10-24) and normally inhibited by TRIM24 (p ¼ 2.6 x10-16).  ...  Methods: Dopamine release was monitored in the nucleus accumbens of rats performing decision making tasks.  ...  editing method.  ... 
doi:10.1038/npp.2014.280 fatcat:xunw4pdn75hlnmhvvksgp2lsse

E‐Poster

2021 Australian and New Zealand journal of obstetrics and gynaecology  
To determine if skinfold measurement could be a costeffective and accessible method to better identify neonates at risk, we compared BF% estimated by skinfolds to PEA POD BF% and birthweight centiles in  ...  She had normal vaginal delivery and live baby boy was delivered. There were no complications in the intrapartum or postpartum period.  ...  There were 1,779 diagnostic tests: 89.6% were performed by microarray and 93 atypical chromosome abnormalities were detected.  ... 
doi:10.1111/ajo.13345 fatcat:svzd22axj5bsfiseapjh77fdje

Introduction to Postmortem Toxicology [chapter]

2007 Postmortem Toxicology of Abused Drugs  
Library of Congress Cataloging-in-Publication Data Postmortem toxicology of abused drugs / [edited by] Steven B. Karch. p. ; cm. "A CRC title." Includes bibliographical references and index.  ...  We now live in the age of the DNA microarray. Chips for measurement of CYP2D6 polymorphisms are already available commercially.  ... 
doi:10.1201/9781420054545-5 fatcat:oadlmkxxwzg4newclnu2ia443u

SU-FF-I-79: Java-Based Plugin for Tomographic Reconstruction for SPECT Data

M Andrade, M Costa, A Marques da Silva
2006 Medical Physics (Lancaster)  
Partially supported by a Varian research grant.  ...  Results: Registration errors are within 0.7mm and 0.1 degree in all cases.  ...  The accuracy of MLS method was compared with that of Wiener-Hopf method in the normalized RMSE values.  ... 
doi:10.1118/1.2240759 fatcat:5we2nvgwx5hrxcv2ngufce6obq

Poster Session II

2015 Neuropsychopharmacology  
Results: RNA from undifferentiated and differentiated iPSC were analyzed using microarray.  ...  By comparing the DNA variation data with the miRNAseq data we found consistent RNA editing of the seed region in three miRNAs: miR-411-5p, miR-376b-3p, and 467d-5p (all of which were A-4I transitions).  ...  To assess and compare the rsFC, we examined and compared the normalized Z maps in group random effect analyses.  ... 
doi:10.1038/npp.2015.326 pmid:26632287 pmcid:PMC4672311 fatcat:ib64i5qmzngvxcpn5hznkcagie

Divergent Responses of Larval and Juvenile Blue Mussels to Low Salinity Exposure

Melissa May, Melissa May, Nikki Adams, Melissa May
2017 Cellular and Molecular Physiology Commons   unpublished
We found that larval mussels differ from juveniles in the composition of their metabolome and in the differential expression of genes involved in the stress response.  ...  divergence in the osmotic stress response.  ...  Changes in BHMT and TAUT expression were analyzed using the DC t method as described in Bustin et al. (2009), normalized to 40S and EF1a.  ... 
fatcat:oz5ulijgfzewvcmchjkv2qlh2u

Impact of plant-based oils and other feed ingredients on growth, tissue composition, gene expression, and health of Atlantic salmon (Salmo salar)

Tomer Katan
2022
In Chapter 3, I used the same fish from the previous feeding trial in order to investigate how the two extreme ω6:ω3 diets (i.e. high ω6 and high ω3) affected the hepatic transcriptome (using 44K microarrays  ...  The microarray study identified transcripts with important roles in lipid metabolism (helz2a), cell proliferation (htra1b), immune and inflammatory response (lect2a, itgb5, helz2a, p43), control of muscle  ...  EPA / DHA) (Phillips, 2012).  ... 
doi:10.48336/wwz3-vk47 fatcat:lgkqs3sw2vfenowa33mmbjzc4a

Abstracts from the Second Astrobiology Science Conference

2002 International Journal of Astrobiology  
(1) The shape and size of the absorption spectra is influenced by O 3 concentrations as well as the temperature in the stratosphere.  ...  Calculations of pO 3 as a function of pO 2 has been done previously by Schindler & Kasting 1 but the temperature profiles in that model were not computed self-consistently.  ...  Mats were maintained in artificial seawater brine containing either : (1) sulfate levels normal for these mats (70 mM), or (2) brine in which sulfate was replaced by chloride.  ... 
doi:10.1017/s147355040200112x fatcat:csnt46qubrce5gwltddgsexgk4
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