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Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

Fenna M. Krienen, B. T. Thomas Yeo, Tian Ge, Randy L. Buckner, Chet C. Sherwood
2016 Proceedings of the National Academy of Sciences of the United States of America  
Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across  ...  Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii  ...  (B) Average distance score for 17 networks, listed along the group-averaged transcriptional similarity matrix for the HSE gene set.  ... 
doi:10.1073/pnas.1510903113 pmid:26739559 pmcid:PMC4739529 fatcat:cmfaupdaovao3kfcvxmiljwf44

Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis

Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong Ho Jung
2007 BMC Bioinformatics  
Conclusion: As an integrative and comprehensive method for the analysis of large-scaled gene expression profiles, our method is able to generate a set of testable hypotheses: the transcriptional regulator  ...  Results: In this study, we propose an algorithm for discovery of molecular functions and elucidation of transcriptional logics using two kinds of gene information, functional and regulatory motif gene  ...  The significance for enrichment of regulatory motif gene sets were also improved in GSECA analysis as shown for 6 and 3 gene sets for myogenesis and erythropoiesis expression profiles, respectively.  ... 
doi:10.1186/1471-2105-8-453 pmid:18021416 pmcid:PMC2217565 fatcat:jaispktjxzbdhnhkxuqm3ecfam

Quantifying the relationship between co-expression, co-regulation and gene function

Dominic J Allocco, Isaac S Kohane, Atul J Butte
2004 BMC Bioinformatics  
In order for two genes to have a greater than 50% chance of sharing a common transcription factor binder, the correlation between their expression profiles (across the 611 microarrays used in our study  ...  in mRNA expression profile or function will be bound by a common transcription factor.  ...  Acknowledgements The authors would like to thank all of the researchers who made publicly available the data used in this study.  ... 
doi:10.1186/1471-2105-5-18 pmid:15053845 pmcid:PMC375525 fatcat:zpa7eb5cbjeghfm3yfhvi5cbse

Mining yeast transcriptional regulatory modules from factor DNA-binding sites and gene expression data

Tho Hoan Pham, Kenji Satou, Tu Bao Ho
2004 Genome Informatics Series  
combinations on sets of genes.  ...  and gene expression profiles data.  ...  Acknowledgments This work was partly supported by a Grant-in-Aid for Scientific Research on Priority Areas (C) "Genome Information Science" from the Ministry of Education, Culture, Sports, Science, and  ... 
pmid:15706514 fatcat:vu6aodh3ajb3nngikmvyq44r3i

Functional annotation and network reconstruction through cross-platform integration of microarray data

Xianghong Jasmine Zhou, Ming-Chih J Kao, Haiyan Huang, Angela Wong, Juan Nunez-Iglesias, Michael Primig, Oscar M Aparicio, Caleb E Finch, Todd E Morgan, Wing Hung Wong
2005 Nature Biotechnology  
Most methods for functional analysis of microarray data make the implicit assumption that genes with similar expression profiles have similar functions 3,4 .  ...  Such a set of four genes, termed a quadruplet, is likely to be functionally related, even though the global expression profiles of those genes do not exhibit gross similarities (see an example in Fig.  ...  ACKNOWLEDGMENTS We thank Robert Gentleman for making his computer resources available for part of this project, Timothy Hughes for technical advice and Michelle Arbeitman for sharing her lab space.  ... 
doi:10.1038/nbt1058 pmid:15654329 fatcat:hpvz6njlf5cftfeapjedzsqv4e

Discovering regulatory binding-site modules using rule-based learning

T. R. Hvidsten
2005 Genome Research  
profiles as measured by, for example, microarray technology.  ...  Transcription factors regulate expression by binding selectively to sequence sites in cis-regulatory regions of genes.  ...  This work was performed in part under the auspices of the U.S.  ... 
doi:10.1101/gr.3760605 pmid:15930496 pmcid:PMC1142476 fatcat:vcpklmk7ofh55fbcyixbb3u35m

Differences in the Early Development of Human and Mouse Embryonic Stem Cells

R. Gabdoulline, W. Kaisers, A. Gaspar, K. Meganathan, M. X. Doss, S. Jagtap, J. Hescheler, A. Sachinidis, H. Schwender, Zhongjun Zhou
2015 PLoS ONE  
The similarity is especially evident, when gene expression profiles are clustered together and properties of clustered groups of genes are compared.  ...  Most of gene groups behave similarly and have similar transcription factor (TF) binding sites on their promoters.  ...  The reason for this is overall similarity of averaged vs single-probe expression profiles for the same gene in our data sets.  ... 
doi:10.1371/journal.pone.0140803 pmid:26473594 pmcid:PMC4608779 fatcat:j3anaoiag5ap7goafdsbbxk7la

The ROS Wheel: Refining ROS Transcriptional Footprints

Patrick Willems, Amna Mhamdi, Simon Stael, Veronique Storme, Pavel Kerchev, Graham Noctor, Kris Gevaert, Frank Van Breusegem
2016 Plant Physiology  
ACKNOWLEDGMENTS We thank Olivier Van Aken and Alessandro Alboresi for providing microarray data available to us and Yvan Saeys for helpful discussions during the course of this research.  ...  Identifying Similar Transcriptional Changes: the ROS Wheel All raw microarray data sets (CEL files) were preprocessed simultaneously, and differential expression of 21,430 genes was calculated for all  ...  For each cluster, the genes differentially expressed in all transcriptional profiles of the respective cluster are presented in Supplemental Table S2 .  ... 
doi:10.1104/pp.16.00420 pmid:27246095 pmcid:PMC4936575 fatcat:wajuwqvswzgz3dzlw4xcrl5zpq

The Pseudomonas aeruginosa Transcriptional Landscape Is Shaped by Environmental Heterogeneity and Genetic Variation

Andreas Dötsch, Monika Schniederjans, Ariane Khaledi, Klaus Hornischer, Sebastian Schulz, Agata Bielecka, Denitsa Eckweiler, Sarah Pohl, Susanne Häussler
2015 mBio  
Our approach allowed dissection of the impact of the genetic background versus environmental cues on P. aeruginosa gene expression profiles and revealed that phenotypic variation was larger in response  ...  We found that gene expression profiles are most strongly influenced by environmental cues, while at the same time the transcriptional profiles were also shaped considerably by genetic variation within  ...  On the other end of the scale, 1,488 genes in the clinical data set and 2,139 genes in the environment data set were found to be transcriptionally active above the sensitivity limit in all transcriptomes  ... 
doi:10.1128/mbio.00749-15 pmid:26126853 pmcid:PMC4488947 fatcat:27dt7wkxsnhf3gr4ecjvhwn6si

Activation of Mitogen-Activated Protein Kinase in Estrogen Receptor α–Positive Breast Cancer CellsIn vitroInduces anIn vivoMolecular Phenotype of Estrogen Receptor α–Negative Human Breast Tumors

Chad J. Creighton, Amy M. Hilger, Shalini Murthy, James M. Rae, Arul M. Chinnaiyan, Dorraya El-Ashry
2006 Cancer Research  
By global mRNA profiling, we found a "MAPK signature" of f400 genes consistently up-regulated or down-regulated in each of the MAPK+ cell lines.  ...  In several independent profile data sets of human breast tumors, the in vitro MAPK signature was able to accurately distinguish ER+ from ERÀ tumors.  ...  Distributions are shown for all profiled genes, for the subset of 153 genes (transcripts) up-regulated in the MAPK signature, and for the 316 genes down-regulated in the MAPK signature.  ... 
doi:10.1158/0008-5472.can-05-4363 pmid:16585219 fatcat:5k5lmritbfazbghfhut33ad5ey

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles [article]

Zhenjia Wang, Mete Civelek, Clint Miller, Nathan Sheffield, Michael J Guertin, Chongzhi Zang
2018 bioRxiv   pre-print
Identification of functional transcription factors that regulate a given gene set is an important problem in gene regulation studies.  ...  Here we present Binding Analysis for Regulation of Transcription (BART), a novel computational method and software package for predicting functional transcription factors that regulate a query gene set  ...  to predict a genome-wide cis-regulatory profile for any query gene set.  ... 
doi:10.1101/280982 fatcat:u4tezyvavjbstozcar4tiexlvy

Page 312 of None Vol. 55, Issue 1 [page]

2007 None  
Sample loadings for the first principal component, which describes 65% of the total variability in expression of these transcripts, demonstrate that the overall expression profile of these transcripts  ...  Sample loadings for the first principal component, which describes 64% of the total variability in gene expression, indicate that the expression profile of developmental genes in mesenteric preadipocytes  ... 

Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding

Hossein Zare, Mostafa Kaveh, Arkady Khodursky
2010 Nature Precedings  
interactions between genes and transcription factors.  ...  We applied KEREN to reconstruct gene regulatory interactions in the model bacteria E.coli on a genome-wide scale.  ...  On the manifold of gene expression, similar expression profiles are points in the local neighborhood of the manifold.  ... 
doi:10.1038/npre.2010.5008 fatcat:wrh4oicngrejfc4et6jihz44jy

Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding

Hossein Zare, Mostafa Kaveh, Arkady Khodursky, Simon Rogers
2011 PLoS ONE  
interactions between genes and transcription factors.  ...  We applied KEREN to reconstruct gene regulatory interactions in the model bacteria E.coli on a genome-wide scale.  ...  On the manifold of gene expression, similar expression profiles are points in the local neighborhood of the manifold.  ... 
doi:10.1371/journal.pone.0021969 pmid:21857910 pmcid:PMC3155518 fatcat:r6kiozzwnnbddlpwxsxf36gspe

Gene expression signatures in childhood acute leukemias are largely unique and distinct from those of normal tissues and other malignancies

Anna Andersson, Patrik Edén, Tor Olofsson, Thoas Fioretos
2010 BMC Medical Genomics  
Gene expression signatures in childhood acute leukemias are largely unique and distinct from those of normal tissues and other malignancies.  ...  Acknowledgements This study was supported by the Swedish Cancer Society, the Swedish Children's Cancer Foundation, the Swedish Research Council, the Medical Faculty of Lund University, the Gunnar Nilsson  ...  This further supports our hypothesis that the gene expression programs that are transcriptionally active in the various subtypes of childhood leukemia are unique to the leukemia and show limited similarity  ... 
doi:10.1186/1755-8794-3-6 pmid:20211010 pmcid:PMC2845086 fatcat:qaoitwoy3vc3ncddtyl2kr64ee
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