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6355 result(s) for 'general transcription factors vs specific' within BMC Genomics

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  1. The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Or...

    Authors: Fuyu Xu, Myoung-Ryoul Park, Ai Kitazumi, Venura Herath, Bijayalaxmi Mohanty, Song Joong Yun and Benildo G de los Reyes
    Citation: BMC Genomics 2012 13:497
    Content type: Research article Published on:

  2. The fasting-refeeding perturbation has been used extensively to reveal specific genes and metabolic pathways that control energy metabolism in the chicken. Most global transcriptional scans of the fasting-refe...

    Authors: Larry A. Cogburn, Nares Trakooljul, Xiaofei Wang, Laura E. Ellestad and Tom E. Porter
    Citation: BMC Genomics 2020 21:109
    Content type: Research article Published on:

  3. Elevated temperatures induce activation of the heat shock transcription factor 1 (HSF1) which in somatic cells leads to heat shock proteins synthesis and cytoprotection. However, in the male germ cells (sperma...

    Authors: Małgorzata Kus-Liśkiewicz, Joanna Polańska, Joanna Korfanty, Magdalena Olbryt, Natalia Vydra, Agnieszka Toma and Wiesława Widłak
    Citation: BMC Genomics 2013 14:456
    Content type: Research article Published on:

  4. Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene famili...

    Authors: Sofia A. Bengoa Luoni, Alberto Cenci, Sebastian Moschen, Salvador Nicosia, Laura M. Radonic, Julia V. Sabio y García, Nicolas B. Langlade, Denis Vile, Cecilia Vazquez Rovere and Paula Fernandez
    Citation: BMC Genomics 2021 22:893
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2022 23:24

  6. Disruption of alveolar epithelial cell (AEC) differentiation is implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that imp...

    Authors: B. Zhou, T. R. Stueve, E. A. Mihalakakos, L. Miao, D. Mullen, Y. Wang, Y. Liu, J. Luo, E. Tran, K. D. Siegmund, S. K. Lynch, A. L. Ryan, I. A. Offringa, Z. Borok and C. N. Marconett
    Citation: BMC Genomics 2021 22:906
    Content type: Research article Published on:

  7. Streptococcus pneumoniae (the pneumococcus) is the world’s foremost microbial pathogen, killing more people each year than HIV, TB or malaria. The capacity to penetrate deeper host tissues contributes substantial...

    Authors: Layla K Mahdi, Tahereh Deihimi, Fatemeh Zamansani, Mario Fruzangohar, David L Adelson, James C Paton, Abiodun D Ogunniyi and Esmaeil Ebrahimie
    Citation: BMC Genomics 2014 15:769
    Content type: Research article Published on:

  9. Our interest in Candida albicans mitochondria began with the identification of GOA1. We demonstrated its role in cell energy production, cross-talk among mitochondria and peroxisomes, non-glucose energy metabolis...

    Authors: Kasra Khamooshi, Patricia Sikorski, Nuo Sun, Richard Calderone and Dongmei Li
    Citation: BMC Genomics 2014 15:56
    Content type: Research article Published on:

  11. In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but al...

    Authors: Alexei A Sharov, Akira Nishiyama, Yulan Piao, Lina S Correa-Cerro, Tomokazu Amano, Marshall Thomas, Samir Mehta and Minoru SH Ko
    Citation: BMC Genomics 2011 12:102
    Content type: Research article Published on:

  12. Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not ...

    Authors: Marty Kwok-Shing Wong, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki and Yoshio Takei
    Citation: BMC Genomics 2014 15:1134
    Content type: Research article Published on:

  13. WRKY transcription factors (TFs) constitute one of the largest protein families in higher plants, and its members contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequen...

    Authors: Xiaosan Huang, Kongqing Li, Xiaoyong Xu, Zhenghong Yao, Cong Jin and Shaoling Zhang
    Citation: BMC Genomics 2015 16:1104
    Content type: Research article Published on:

  15. Gene expression is to large degree regulated by the specific binding of protein transcription factors to cis-regulatory transcription factor binding sites in gene promoter regions. Despite the identification o...

    Authors: Monika Lis and Dirk Walther
    Citation: BMC Genomics 2016 17:185
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2016 17:310

  16. ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relative...

    Authors: Jiali Song, Changming Chen, Shuanglin Zhang, Juntao Wang, Zhubing Huang, Muxi Chen, Bihao Cao, Zhangsheng Zhu and Jianjun Lei
    Citation: BMC Genomics 2020 21:573
    Content type: Research article Published on:

  17. Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that...

    Authors: Alena Myšičková and Martin Vingron
    Citation: BMC Genomics 2012 13(Suppl 1):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  18. Sharing a common ErbB/HER receptor signaling pathway, heregulin (HRG) induces differentiation of MCF-7 human breast cancer cells while epidermal growth factor (EGF) elicits proliferation. Although cell fates r...

    Authors: Yuko Saeki, Takaho Endo, Kaori Ide, Takeshi Nagashima, Noriko Yumoto, Tetsuro Toyoda, Harukazu Suzuki, Yoshihide Hayashizaki, Yoshiyuki Sakaki and Mariko Okada-Hatakeyama
    Citation: BMC Genomics 2009 10:545
    Content type: Research article Published on:

  19. A major production constraint on the important ornamental species chrysanthemum is black spot which is caused by the necrotrophic fungus Alternaria tenuissima. The molecular basis of host resistance to A. tenuiss...

    Authors: Huiyun Li, Sumei Chen, Aiping Song, Haibin Wang, Weimin Fang, Zhiyong Guan, Jiafu Jiang and Fadi Chen
    Citation: BMC Genomics 2014 15:9
    Content type: Research article Published on:

  20. To date, only a few transcription factors have been identified in the genome of the parasite Plasmodium falciparum, the causative agent of malaria. Moreover, no detailed molecular analysis of its basal transcript...

    Authors: Isabelle Callebaut, Karine Prat, Edwige Meurice, Jean-Paul Mornon and Stanislas Tomavo
    Citation: BMC Genomics 2005 6:100
    Content type: Research article Published on:

  21. Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA bind...

    Authors: Shalev Itzkovitz, Tsvi Tlusty and Uri Alon
    Citation: BMC Genomics 2006 7:239
    Content type: Research article Published on:

  22. Aglaonema commutatum ‘Red Valentine’, as a foliage ornamental plant, is widely used for interior and exterior decoration because of its easy cultivation and management. However, reduced proportion of red foliage ...

    Authors: Ji Li, Kunlin Wu, Lin Li, Guohua Ma, Lin Fang and Songjun Zeng
    Citation: BMC Genomics 2023 24:28
    Content type: Research Published on:

  23. Salmonella enterica serovar typhimurium is the cause of significant morbidity and mortality worldwide that causes economic losses to poultry and is able to cause infection in humans. Indigenous chicken breeds are...

    Authors: Syed Mudasir Ahmad, Sahar Saleem Bhat, Shaista Shafi, Mashooq Ahmad Dar, Afnan Saleem, Zulfqarul Haq, Nida Farooq, Junaid Nazir and Basharat Bhat
    Citation: BMC Genomics 2023 24:214
    Content type: Research Published on:

  26. The analysis of differential gene expression is a fundamental tool to relate gene regulation with specific biological processes. Differential binding of transcription factors (TFs) can drive differential gene ...

    Authors: Jason Piper, Salam A. Assi, Pierre Cauchy, Christophe Ladroue, Peter N. Cockerill, Constanze Bonifer and Sascha Ott
    Citation: BMC Genomics 2015 16:1000
    Content type: Methodology article Published on:

  27. Basic leucine zipper (bZIP) transcription factors are present exclusively in eukaryotes and constitute one of the largest and most diverse transcription factor families. The proteins are responsible for centra...

    Authors: Wenwu Ye, Yang Wang, Suomeng Dong, Brett M Tyler and Yuanchao Wang
    Citation: BMC Genomics 2013 14:839
    Content type: Research article Published on:

  28. Genetic alterations of transcription factors (TFs) have been implicated in the tumorigenesis of cancers. In many cancers, alteration of TFs results in aberrant activity of them without changing their gene expr...

    Authors: Mingzhu Zhu, Chun-Chi Liu and Chao Cheng
    Citation: BMC Genomics 2013 14:504
    Content type: Methodology article Published on:

  29. The cellular response to ionizing radiation involves activation of p53-dependent pathways and activation of the atypical NF-κB pathway. The crosstalk between these two transcriptional networks include (co)regu...

    Authors: Katarzyna Szołtysek, Patryk Janus, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Simon Cockell, Neil D. Perkins, Marek Kimmel and Piotr Widlak
    Citation: BMC Genomics 2018 19:813
    Content type: Research article Published on:

  30. Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contex...

    Authors: Shan Zhong, Xin He and Ziv Bar-Joseph
    Citation: BMC Genomics 2013 14:796
    Content type: Methodology article Published on:

  32. Alzheimer’s disease (AD) is intimately tied to amyloid-β (Aβ) peptide. Extraneuronal brain plaques consisting primarily of Aβ aggregates are a hallmark of AD. Intraneuronal Aβ subunits are strongly implicated ...

    Authors: Debomoy K Lahiri, Bryan Maloney, Jack T Rogers and Yuan-Wen Ge
    Citation: BMC Genomics 2013 14:68
    Content type: Research article Published on:

  33. Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal gen...

    Authors: Richard B Todd, Miaomiao Zhou, Robin A Ohm, Hendrika ACF Leeggangers, Loek Visser and Ronald P de Vries
    Citation: BMC Genomics 2014 15:214
    Content type: Research article Published on:

  34. A variety of protocols exist for producing whole genome run-on transcription datasets. However, little is known about how differences between these protocols affect the signal within the resulting libraries.

    Authors: Samuel Hunter, Rutendo F. Sigauke, Jacob T. Stanley, Mary A. Allen and Robin D. Dowell
    Citation: BMC Genomics 2022 23:187
    Content type: Research Published on:

  35. The Fra-1/AP-1 transcription factor regulates the expression of genes controlling various processes including migration, invasion, and survival as well as extracellular remodeling. We recently demonstrated tha...

    Authors: Subbiah Rajasekaran, Narsa M Reddy, Wei Zhang and Sekhar P Reddy
    Citation: BMC Genomics 2013 14:381
    Content type: Research article Published on:

  36. Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV, and gamma radiation. Dynamic alte...

    Authors: Kriti Sharma, Nicholas Gillum, J Lomax Boyd and Amy Schmid
    Citation: BMC Genomics 2012 13:351
    Content type: Research article Published on:

  37. Brugia malayi is a nematode parasite that causes lymphatic filariasis, a disfiguring and disabiling tropical disease. Although a first draft genome sequence was released in 2007, very little is understood about t...

    Authors: Ben-Wen Li, Zhengyuan Wang, Amy C Rush, Makedonka Mitreva and Gary J Weil
    Citation: BMC Genomics 2012 13:184
    Content type: Research article Published on:

  38. Cis-regulatory modules are bound by transcription factors to regulate gene expression. Characterizing these DNA sequences is central to understanding gene regulatory networks and gaining insight into mechanisms o...

    Authors: Marc S Halfon, Qianqian Zhu, Elizabeth R Brennan and Yiyun Zhou
    Citation: BMC Genomics 2011 12:578
    Content type: Research article Published on:

  39. In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conse...

    Authors: Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier and Laurent Bréhélin
    Citation: BMC Genomics 2019 20:103
    Content type: Methodology article Published on:

  42. Spore germination of the yeast Saccharomyces cerevisiae is a multi-step developmental path on which dormant spores re-enter the mitotic cell cycle and resume vegetative growth. Upon addition of a fermentable carb...

    Authors: Cecilia Geijer, Ivan Pirkov, Wanwipa Vongsangnak, Abraham Ericsson, Jens Nielsen, Marcus Krantz and Stefan Hohmann
    Citation: BMC Genomics 2012 13:554
    Content type: Research article Published on:

  43. Nr2e1 (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundr...

    Authors: Jean-François Schmouth, David Arenillas, Ximena Corso-Díaz, Yuan-Yun Xie, Slavita Bohacec, Kathleen G. Banks, Russell J. Bonaguro, Siaw H. Wong, Steven J. M. Jones, Marco A. Marra, Elizabeth M. Simpson and Wyeth W. Wasserman
    Citation: BMC Genomics 2015 16:545
    Content type: Research article Published on:

  44. The neonatal bovine mammary fat pad (MFP) surrounding the mammary parenchyma (PAR) is thought to exert proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones...

    Authors: Paola Piantoni, Massimo Bionaz, Daniel E Graugnard, Kristy M Daniels, Robin E Everts, Sandra L Rodriguez-Zas, Harris A Lewin, Hurley L Hurley, Michael Akers and Juan J Loor
    Citation: BMC Genomics 2010 11:331
    Content type: Research article Published on:

  45. A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis ...

    Authors: Yong-Mei Bi, Rong-Lin Wang, Tong Zhu and Steven J Rothstein
    Citation: BMC Genomics 2007 8:281
    Content type: Research article Published on:

  46. High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS pro...

    Authors: Michael P. Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay and A. Gregory Matera
    Citation: BMC Genomics 2018 19:157
    Content type: Research article Published on:

  47. Malaria is the most important parasitic disease in the world with approximately two million people dying every year, mostly due to Plasmodium falciparum infection. During its complex life cycle in the Anopheles v...

    Authors: Emmanuel Bischoff and Catherine Vaquero
    Citation: BMC Genomics 2010 11:34
    Content type: Research article Published on:

  48. ChIP-Seq is widely used to detect genomic segments bound by transcription factors (TF), either directly at DNA binding sites (BSs) or indirectly via other proteins. Currently, there are many software tools imp...

    Authors: Victor G Levitsky, Ivan V Kulakovskiy, Nikita I Ershov, Dmitry Yu Oshchepkov, Vsevolod J Makeev, T C Hodgman and Tatyana I Merkulova
    Citation: BMC Genomics 2014 15:80
    Content type: Research article Published on:

  49. The sequence content of the 3′ UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging.

    Authors: Raeann Goering, Krysta L. Engel, Austin E. Gillen, Nova Fong, David L. Bentley and J. Matthew Taliaferro
    Citation: BMC Genomics 2021 22:476
    Content type: Methodology article Published on:

  50. Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the co...

    Authors: Yu Bai, Emmanuel Caussinus, Stefano Leo, Fritz Bosshardt, Faina Myachina, Gregor Rot, Mark D. Robinson and Christian F. Lehner
    Citation: BMC Genomics 2021 22:771
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2022 23:241

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