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Page 388 of Cellular and Molecular Life Sciences Vol. 64, Issue 4 [page]

2007 Cellular and Molecular Life Sciences  
Signatures of promoters The diverse approaches to promoter identification de- scribed above have provided unprecedented resources for large-scale promoter characterization.  ...  Numerous re- sources and techniques now contribute to the large-scale study and analysis of an ever-expanding library of eu- karyotic promoters.  ... 

A regulatory toolbox of MiniPromoters to drive selective expression in the brain

E. Portales-Casamar, D. J. Swanson, L. Liu, C. N. d. Leeuw, K. G. Banks, S. J. Ho Sui, D. L. Fulton, J. Ali, M. Amirabbasi, D. J. Arenillas, N. Babyak, S. F. Black (+52 others)
2010 Proceedings of the National Academy of Sciences of the United States of America  
The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters and related tools  ...  The availability of a large collection of new MiniPs will play an important role in research and treatment for incurable brain diseases.  ... 
doi:10.1073/pnas.1009158107 pmid:20807748 pmcid:PMC2944712 fatcat:bhtgrkwzqjbjjplh6quo55nvda

MON-719 The Cellular and Molecular Landscape of Hypothalamic Patterning and Differentiation

Thomas Kim
2020 Journal of the Endocrine Society  
We likewise observed clean segregation among cells expressing regional hypothalamic markers identified in previous large-scale analysis of hypothalamic development.  ...  We aim to use this knowledge and information of key molecular pathways of human hypothalamic development and produce human hypothalamus organoids.  ...  We likewise observed clean segregation among cells expressing regional hypothalamic markers identified in previous large-scale analysis of hypothalamic development.  ... 
doi:10.1210/jendso/bvaa046.1237 fatcat:lyqv4jlqbbds5dwjg2kev4hxhq

Paradigm shifts in genomics through the FANTOM projects

Michiel de Hoon, Jay W. Shin, Piero Carninci
2015 Mammalian Genome  
The FANTOM Consortium has provided the most comprehensive mouse cDNA collection for functional studies and extensive maps of the human and mouse transcriptome comprising promoters, enhancers, as well as  ...  We argue that large-scale studies are urgently needed to address the functional role of lncRNAs.  ...  Acknowledgments We are indebted with all the members of the FANTOM consortium and RIKEN colleagues, in particular at RIKEN Center for Life Science Technologies and RIKEN PMI.  ... 
doi:10.1007/s00335-015-9593-8 pmid:26253466 pmcid:PMC4602071 fatcat:7y5if7dg7fao3pp6wogpducl2y

PRESTA: associating promoter sequences with information on gene expression

Václav Mach
2002 Genome Biology  
The current size of this resource is 552 human and 241 mouse promoters.  ...  Large sets of well-characterized promoter sequences are required to facilitate the understanding of promoter architecture.  ...  These utilities are not, however, linked to gene promoter sequences and therefore not readily useful for large-scale studies of promoter expression.  ... 
pmid:12225589 pmcid:PMC126875 fatcat:ytep37u4dnajxj6563s5fedxia

Mouse phenogenomics, toolbox for functional annotation of human genome

Il-Yong Kim, Jae-Hoon Shin, Je-Kyung Seong
2010 BMB Reports  
However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing  ...  Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of  ...  Large scale production of GEM Three major mouse knockout programs are underway worldwide, working together to mutate all protein-encoding genes in the mouse using a combination of gene trapping and gene  ... 
doi:10.5483/bmbrep.2010.43.2.079 pmid:20193125 fatcat:wofaujx5m5dn7pu2s7lelqxxfa

Distinct class of putative "non-conserved" promoters in humans: Comparative studies of alternative promoters of human and mouse genes

K. Tsuritani, T. Irie, R. Yamashita, Y. Sakakibara, H. Wakaguri, A. Kanai, J. Mizushima-Sugano, S. Sugano, K. Nakai, Y. Suzuki
2007 Genome Research  
Here we report large-scale comparative studies of PAPs between human and mouse counterpart genes.  ...  Detailed sequence comparison of the 17,245 putative promoter regions (PPRs) in 5463 PAP-containing human genes revealed that PPRs in only a minor fraction of genes (807 genes) showed clear evolutionary  ...  Center project of METI of JAPAN; and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports, and Culture of Japan.  ... 
doi:10.1101/gr.6030107 pmid:17567985 pmcid:PMC1899111 fatcat:2zc6mevh5za4npihjsxu3kojw4

Viral Vectors as Part of an Integrated Functional Genomics Program

Janson G. Christopher, Matthew J. During
2001 Genomics  
Over the past decade, viral vectors have slowly gained mainstream acceptance in the neuroscience and genetics communities for the in vivo study of gene function [1].  ...  The effects of gene expression in the brain can be measured on the molecular, biochemical, electrophysiological, morphological, and behavioral levels.  ...  An important limitation of whole-genome mouse knockouts is that the mouse genome is not strictly homologous to the human genome and thus certain genes cannot be tested.  ... 
doi:10.1006/geno.2001.6653 pmid:11707065 fatcat:246ksh5q3nhfxde56igpo4igiu

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair RR Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub
2009 Genome Biology  
time course of the human THP-1 cell line and under 52 systematic siRNA perturbations.  ...  In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation  ...  F Hori for information collection.  ... 
doi:10.1186/gb-2009-10-4-r40 pmid:19374775 pmcid:PMC2688931 fatcat:3cjsi66kv5f6pohusyurdqiloy

Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency

Rodolfo Gonzalez, Lori L. Jennings, Mark Knuth, Anthony P. Orth, Heath E. Klock, Weija Ou, Julie Feuerhelm, Mitchell V. Hull, Eric Koesema, Yuping Wang, Jia Zhang, Chunlei Wu (+11 others)
2010 Proceedings of the National Academy of Sciences of the United States of America  
Predicted secreted gene lists were compiled from previous large-scale efforts including the secreted protein discovery initiative (SPDI) (10) and the web-based  ...  To analyze the physiological activities of the extracellular proteome, we developed a large-scale, high-throughput protein expression, purification, and screening platform.  ...  Cloning efforts were supported in part by National Institutes of Health Grant U54 GM074898 (Joint Center for Structural Genomics) from the National Institute of General Medical Sciences.  ... 
doi:10.1073/pnas.0914019107 pmid:20133595 pmcid:PMC2840467 fatcat:q3q674me65apvjuncngffxhlhu

Microglia-Specific Promoter Activities of HEXB Gene

Sahil Shah, Lilly M. Wong, Kendra Ellis, Brittany Bodnar, Sami Saribas, Julia Ting, Zhengyu Wei, Yuyang Tang, Xianwei Wang, Hong Wang, Binhua Ling, David M. Margolis (+3 others)
2022 Frontiers in Cellular Neuroscience  
The native promoter region of mouse, human, and monkey HEXB are located at −135, −134, and −170 bp to the first ATG, respectively.  ...  Here, we characterized the minimal/native promoter of the HEXB gene, which is known to be specifically and stably expressed in the microglia during homeostatic and pathological conditions.  ...  Cloning and Characterization of Essential Promoter Regions for Human and Rhesus Macaque HEXB Because of the high level of sequence conservation across species in the promoter region of HEXB genes (Bapat  ... 
doi:10.3389/fncel.2022.808598 pmid:35360489 pmcid:PMC8960132 fatcat:d2oz5y6bojfdvmdaon7fghe454

New Products

2010 Science  
and either human or mouse agilent promoter microarrays.  ...  more than 700 human and human-viral mirnas with a specificity and sensitivity comparable to quantitative Pcr. the assay kit contains all of the reagents and consumables required to conduct mirna and gene  ... 
doi:10.1126/science.329.5990.466-a fatcat:ibkuopx3h5bj7err5jo3p5iz3e

Cre recombinase resources for conditional mouse mutagenesis

Damian Smedley, Ekaterina Salimova, Nadia Rosenthal
2011 Methods  
Large scale international activities for systematic conditional mouse mutagenesis, exploiting advances in the sophisticated manipulation of the mouse genome, has established the mouse as the premier organism  ...  for developing models of human disease and drug action.  ...  Acknowledgments We thank members of the CREATE consortium for their participation and contributions:  ... 
doi:10.1016/j.ymeth.2010.12.027 pmid:21195764 fatcat:itx3zx23czbkrp5237y5jodrue

Distal enhancers: new insights into heart development and disease

Joseph A. Wamstad, Xinchen Wang, Olukunle O. Demuren, Laurie A. Boyer
2014 Trends in Cell Biology  
Large-scale studies have recently identified hundreds of thousands of distal enhancer elements; their discovery has revealed new insights into the mechanistic details of how tissue-specific gene expression  ...  Emerging evidence indicates that lineage-specific transcription factors and chromatin regulators coordinate the activation of distal enhancers to ensure robust control of gene expression programs in a  ...  Acknowledgments We are grateful to members of the Boyer laboratory for insightful discussions and to the investigators in the field whose collective works have inspired a new era in biology.  ... 
doi:10.1016/j.tcb.2013.10.008 pmid:24321408 fatcat:lx7tcfcli5gufbobzt3pyftf34

PromoSer: a large-scale mammalian promoter and transcription start site identification service

A. S. Halees
2003 Nucleic Acids Research  
Studies of the sequencebased nature of this regulation usually require collection of proximal promoter sequences for large sets of co-regulated genes.  ...  We report a newly implemented web service that facilitates extraction of user specified regions around the transcription start site of all annotated human, mouse or rat genes.  ...  ACKNOWLEDGEMENTS We wish to thank Martin Frith, Peter Haverty and Joel Graber for thought provoking discussions and advice and the sharing of helpful resources.  ... 
doi:10.1093/nar/gkg549 pmid:12824364 pmcid:PMC168956 fatcat:prn3aou74nhwpkbcdryxqmo55a
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