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

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  1. Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode Caenorhabditis elegans is an establ...

    Authors: Wilfried Haerty, Carlo Artieri, Navid Khezri, Rama S Singh and Bhagwati P Gupta
    Citation: BMC Genomics 2008 9:399
    Content type: Research article Published on:

  2. As a polycistronic transcriptional unit of one or more adjacent genes, operons play a key role in regulation and function in prokaryotic biology, and a better understanding of how they are constituted and cont...

    Authors: Emma Laing, Khushwant Sidhu and Simon J Hubbard
    Citation: BMC Genomics 2008 9:79
    Content type: Research article Published on:

  3. The mitochondria are central in the cellular response to changing environmental conditions resulting from disease states, environmental exposures or normal physiological processes. Although the influences of e...

    Authors: John Lees, Fábio Pèrtille, Pia Løtvedt, Per Jensen and Carlos Guerrero Bosagna
    Citation: BMC Genomics 2023 24:561
    Content type: Research Published on:

  4. The motif ACTAYRNNNCCCR (Y being C or T, R being A or G, and N any nucleotide), called M4, was discovered as a putative cis-regulatory element, present 520 times in human promoter regions. Of these, 317 (61 %)...

    Authors: Ngo Tat Trung, Elisabeth Kremmer and Gerhard Mittler
    Citation: BMC Genomics 2016 17:693
    Content type: Research article Published on:

  5. The ability of plants to withstand and thrive in an adverse environment is crucial to ensure their survivability and yield performance. The WRKY transcription factors (TFs) have crucial roles in plant growth, ...

    Authors: Fong Chin Lee, Wan Chin Yeap, David Ross Appleton, Chai-Ling Ho and Harikrishna Kulaveerasingam
    Citation: BMC Genomics 2022 23:164
    Content type: Research Published on:

  6. The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies great...

    Authors: Amos A. Schaffer, Michael Bazarsky, Karine Levy, Vered Chalifa-Caspi and Uri Gat
    Citation: BMC Genomics 2016 17:718
    Content type: Research article Published on:

  7. A major constraint affecting the quality and productivity of chrysanthemum is the unusual period of low temperature occurring during early spring, late autumn, and winter. Yet, there has been no systematic inv...

    Authors: Liping Ren, Jing Sun, Sumei Chen, Jiaojiao Gao, Bin Dong, Yanan Liu, Xiaolong Xia, Yinjie Wang, Yuan Liao, Nianjun Teng, Weimin Fang, Zhiyong Guan, Fadi Chen and Jiafu Jiang
    Citation: BMC Genomics 2014 15:844
    Content type: Research article Published on:

  8. Inflammation triggered by infection or injury is tightly controlled by glucocorticoid hormones which signal via a dedicated transcription factor, the Glucocorticoid Receptor (GR), to regulate hundreds of genes...

    Authors: Yurii Chinenov, Maddalena Coppo, Rebecca Gupte, Maria A Sacta and Inez Rogatsky
    Citation: BMC Genomics 2014 15:656
    Content type: Research article Published on:

  9. Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes. In contrast, the identification of the transcription factors (TFs) interacting w...

    Authors: Christian Dubos, Zsolt Kelemen, Alvaro Sebastian, Lorenz Bülow, Gunnar Huep, Wenjia Xu, Damaris Grain, Fabien Salsac, Cecile Brousse, Loïc Lepiniec, Bernd Weisshaar, Bruno Contreras-Moreira and Reinhard Hehl
    Citation: BMC Genomics 2014 15:317
    Content type: Research article Published on:

  10. Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors ...

    Authors: Chia-Chun Yang, Erik H. Andrews, Min-Hsuan Chen, Wan-Yu Wang, Jeremy J. W. Chen, Mark Gerstein, Chun-Chi Liu and Chao Cheng
    Citation: BMC Genomics 2016 17:632
    Content type: Database Published on:

  11. Hypocrea jecorina (anamorph Trichoderma reesei) is a filamentous ascomycete of industrial importance due to its hydrolases (e.g., xylanases and cellulases). The regulation of gene expression can influence the com...

    Authors: Astrid R Mach-Aigner, Karin Grosstessner-Hain, Marcio J Poças-Fonseca, Karl Mechtler and Robert L Mach
    Citation: BMC Genomics 2010 11:644
    Content type: Methodology article Published on:

  12. Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in Populus deltoids has not ye...

    Authors: Xiao-jing Wang, Xu-qian Peng, Xiao-chun Shu, Yu-hang Li, Zhong Wang and Wei-bing Zhuang
    Citation: BMC Genomics 2022 23:244
    Content type: Research Published on:

  14. Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important m...

    Authors: Jan-Philip Schlüter, Jan Reinkensmeier, Melanie J Barnett, Claus Lang, Elizaveta Krol, Robert Giegerich, Sharon R Long and Anke Becker
    Citation: BMC Genomics 2013 14:156
    Content type: Research article Published on:

  15. Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the emb...

    Authors: Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang and Harold B. White III
    Citation: BMC Genomics 2018 19:695
    Content type: Research article Published on:

  16. Characterization of cellular growth is central to understanding living systems. Here, we applied a three-factor design to study the relationship between specific growth rate and genome-wide gene expression in ...

    Authors: Alessandro Fazio, Michael C Jewett, Pascale Daran-Lapujade, Roberta Mustacchi, Renata Usaite, Jack T Pronk, Christopher T Workman and Jens Nielsen
    Citation: BMC Genomics 2008 9:341
    Content type: Research article Published on:

  17. Post-translational modification (PTM) of transcriptional factors and chromatin remodelling proteins is recognized as a major mechanism by which transcriptional regulation occurs. Chromatin immunoprecipitation ...

    Authors: Chia-Yang Cheng, Chia-Han Chu, Hung-Wei Hsu, Fang-Rong Hsu, Chung Yi Tang, Wen-Ching Wang, Hsing-Jien Kung and Pei-Ching Chang
    Citation: BMC Genomics 2014 15(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 1

  18. The transcription factor (TF) forkhead box P3 (FOXP3) is constitutively expressed at high levels in naturally occurring CD4+CD25+ regulatory T cells (nTregs). It is not only the most accepted marker for that cell...

    Authors: Andreas Jeron, Wiebke Hansen, Franziska Ewert, Jan Buer, Robert Geffers and Dunja Bruder
    Citation: BMC Genomics 2012 13:705
    Content type: Research article Published on:

  19. In the last few years several studies have shown that Transposable Elements (TEs) in the human genome are significantly associated with Transcription Factor Binding Sites (TFBSs) and that in several cases thei...

    Authors: Alessandro Testori, Livia Caizzi, Santina Cutrupi, Olivier Friard, Michele De Bortoli, Davide Cora' and Michele Caselle
    Citation: BMC Genomics 2012 13:400
    Content type: Research article Published on:

  20. Glandular trichomes are production and storage organs of specialized metabolites such as terpenes, which play a role in the plant’s defense system. The present study aimed to shed light on the regulation of te...

    Authors: Eleni A Spyropoulou, Michel A Haring and Robert C Schuurink
    Citation: BMC Genomics 2014 15:402
    Content type: Research article Published on:

  21. Anaplasma phagocytophilum (Ap) is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of ce...

    Authors: Curtis M Nelson, Michael J Herron, Roderick F Felsheim, Brian R Schloeder, Suzanne M Grindle, Adela Oliva Chavez, Timothy J Kurtti and Ulrike G Munderloh
    Citation: BMC Genomics 2008 9:364
    Content type: Research article Published on:

  22. Transcription factors (TFs) contain DNA-binding domains (DBDs) and regulate gene expression by binding to specific DNA sequences. In addition, there are proteins, called transcription coregulators (TCs), which...

    Authors: Jinn-Jy Lin, Chun-Ping Yu, Yao-Ming Chang, Sean Chun-Chang Chen and Wen-Hsiung Li
    Citation: BMC Genomics 2014 15:818
    Content type: Research article Published on:

  23. Aroclor 1254 is a well-known hepatotoxin and consists of a complex mixture of polychlorinated biphenyls (PCBs), some of which have the ability to activate the aryl hydrocarbon receptor (AhR) and other transcri...

    Authors: Susanne Reymann and Jürgen Borlak
    Citation: BMC Genomics 2006 7:217
    Content type: Research article Published on:

  24. When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relat...

    Authors: Zhichi Zeng, Sichen Zhang, Wenyan Li, Baoshan Chen and Wenlan Li
    Citation: BMC Genomics 2022 23:251
    Content type: Research Published on:

  25. The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (Pyrus brestschneideri Rehd). Flowers were collected at early bloom, full bloo...

    Authors: Maosong Pei, Jianxin Niu, Chenjing Li, Fujun Cao and Shaowen Quan
    Citation: BMC Genomics 2016 17:132
    Content type: Research article Published on:

  26. In the post-genomic era, comprehension of cellular processes and systems requires global and non-targeted approaches to handle vast amounts of biological information.

    Authors: Hirokazu Kobayashi, Joe Akitomi, Nobuyuki Fujii, Kazuo Kobayashi, Md Altaf-Ul-Amin, Ken Kurokawa, Naotake Ogasawara and Shigehiko Kanaya
    Citation: BMC Genomics 2007 8:197
    Content type: Research article Published on:

  27. The majority of the genes involved in the inflammatory response are highly conserved in mammals. These genes are not significantly expressed under normal conditions and are mainly regulated at the transcriptio...

    Authors: Daniel Rico, Juan M Vaquerizas, Hernán Dopazo and Lisardo Boscá
    Citation: BMC Genomics 2007 8:271
    Content type: Research article Published on:

  28. Lymphotoxin signaling via the lymphotoxin-β receptor (LTβR) has been implicated in biological processes ranging from development of secondary lymphoid organs, maintenance of spleen architecture, host defense a...

    Authors: Agnes Lovas, Dörte Radke, Daniela Albrecht, Z Buket Yilmaz, Ulrich Möller, Andreas JR Habenicht and Falk Weih
    Citation: BMC Genomics 2008 9:606
    Content type: Research article Published on:

  30. The CSL (C BF1/RBP-Jκ/S uppressor of Hairless/L AG-1) transcription factor family members are well-known components of the transmembrane receptor Notch signaling pathway, which plays a critical role in metazoan d...

    Authors: Martin Převorovský, František Půta and Petr Folk
    Citation: BMC Genomics 2007 8:233
    Content type: Research article Published on:

  31. Early aerial senescence in switchgrass (Panicum virgatum) can significantly limit biomass yields. WRKY transcription factors that can regulate senescence could be used to reprogram senescence and enhance biomass ...

    Authors: Charles I. Rinerson, Erin D. Scully, Nathan A. Palmer, Teresa Donze-Reiner, Roel C. Rabara, Prateek Tripathi, Qingxi J Shen, Scott E. Sattler, Jai S. Rohila, Gautam Sarath and Paul J. Rushton
    Citation: BMC Genomics 2015 16:912
    Content type: Research article Published on:

  32. More than 80 % of all terrestrial plant species establish an arbuscular mycorrhiza (AM) symbiosis with Glomeromycota fungi. This plant-microbe interaction primarily improves phosphate uptake, but also supports ni...

    Authors: Natalija Hohnjec, Lisa F. Czaja-Hasse, Claudia Hogekamp and Helge Küster
    Citation: BMC Genomics 2015 16:994
    Content type: Research article Published on:

  33. Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining.

    Authors: Carlos Alberto Oliveira de Biagi Jr, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo and Wilson Araújo Silva Jr
    Citation: BMC Genomics 2021 22:624
    Content type: Software Published on:

  34. The human genome contains a large amount of cis-regulatory DNA elements responsible for directing both spatial and temporal gene-expression patterns. Previous studies have shown that based on their mRNA expressio...

    Authors: Himanshu Joshi, Silje H Nord, Arnoldo Frigessi, Anne-Lise Børresen-Dale and Vessela N Kristensen
    Citation: BMC Genomics 2012 13:199
    Content type: Research article Published on:

  35. HacA/Xbp1 is a conserved bZIP transcription factor in eukaryotic cells which regulates gene expression in response to various forms of secretion stress and as part of secretory cell differentiation. In the pre...

    Authors: Neuza DSP Carvalho, Thomas R Jørgensen, Mark Arentshorst, Benjamin M Nitsche, Cees AMJJ van den Hondel, David B Archer and Arthur FJ Ram
    Citation: BMC Genomics 2012 13:350
    Content type: Research article Published on:

  36. Renal inflammation plays a crucial role during the progression of Chronic kidney disease (CKD), but there is limited research on hub genes involved in renal inflammation. Here, we aimed to explore the effects ...

    Authors: Jing Chen, Yuwei Liu, Shang Xia, Xujun Ye and Ling Chen
    Citation: BMC Genomics 2022 23:544
    Content type: Research article Published on:

  37. Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in pea...

    Authors: Zhihui Wang, Liying Yan, Liyun Wan, Dongxin Huai, Yanping Kang, Lei Shi, Huifang Jiang, Yong Lei and Boshou Liao
    Citation: BMC Genomics 2019 20:51
    Content type: Research article Published on:

  38. It is well known that carcinogenesis is in part dictated by dysregulated transcription events and signal pathways. Large-scale transcriptional profiling studies in each cancer type have reported aberrant gene ...

    Authors: Jing Wang, Qi Liu and Yu Shyr
    Citation: BMC Genomics 2015 16(Suppl 7):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  39. Classically, models of DNA-transcription factor binding sites (TFBSs) have been based on relatively few known instances and have treated them as sites of fixed length using position weight matrices (PWMs). Var...

    Authors: John E Reid, Kenneth J Evans, Nigel Dyer, Lorenz Wernisch and Sascha Ott
    Citation: BMC Genomics 2010 11:30
    Content type: Research article Published on:

  40. Porcine circovirus type 2 (PCV2) is the causal agent of postweaning multisystemic wasting syndrome (PMWS), which has severely impacted the swine industry worldwide. PCV2 triggers a weak and atypical innate imm...

    Authors: Wentao Li, Shuqing Liu, Yang Wang, Feng Deng, Weidong Yan, Kun Yang, Huanchun Chen, Qigai He, Catherine Charreyre and Jean-Christophe Audoneet
    Citation: BMC Genomics 2013 14:353
    Content type: Research article Published on:

  41. Plant growth and development can be significantly impacted by drought stress. Plants will adjust the synthesis and accumulation of secondary metabolites to improve survival in times of water constraint. Simult...

    Authors: Shuo Wang, XueLei Zhao, Chang Li, Jing Dong, JiaCheng Ma, YueHong Long and ZhaoBin Xing
    Citation: BMC Genomics 2024 25:330
    Content type: Research Published on:

  42. Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a who...

    Authors: Aline S. M. Cesar, Luciana C. A. Regitano, James M. Reecy, Mirele D. Poleti, Priscila S. N. Oliveira, Gabriella B. de Oliveira, Gabriel C. M. Moreira, Maurício A. Mudadu, Polyana C. Tizioto, James E. Koltes, Elyn Fritz-Waters, Luke Kramer, Dorian Garrick, Hamid Beiki, Ludwig Geistlinger, Gerson B. Mourão…
    Citation: BMC Genomics 2018 19:499
    Content type: Research article Published on:

  43. Gene expression is regulated mainly by transcription factors (TFs) that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements, computer searching can predict TF bindin...

    Authors: Katsuhiko Murakami, Toshio Kojima and Yoshiyuki Sakaki
    Citation: BMC Genomics 2004 5:16
    Content type: Research article Published on:

  44. Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, d...

    Authors: Atit Parajuli, Bhabesh Borphukan, Karen A. Sanguinet and Zhiwu Zhang
    Citation: BMC Genomics 2024 25:497
    Content type: Research Published on:

  45. Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix–lo...

    Authors: Miyako Kodama, Henrik Brinch-Pedersen, Shrikant Sharma, Inger Bæksted Holme, Bjarne Joernsgaard, Tsaneta Dzhanfezova, Daniel Buchvaldt Amby, Filipe Garrett Vieira, Shanlin Liu and M Thomas P Gilbert
    Citation: BMC Genomics 2018 19:811
    Content type: Research article Published on:

  46. Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is a...

    Authors: Marcela Mendes Salazar, Leandro Costa Nascimento, Eduardo Leal Oliveira Camargo, Danieli Cristina Gonçalves, Jorge Lepikson Neto, Wesley Leoricy Marques, Paulo José Pereira Lima Teixeira, Piotr Mieczkowski, Jorge Maurício Costa Mondego, Marcelo Falsarella Carazzolle, Ana Carolina Deckmann and Gonçalo Amarante Guimarães Pereira
    Citation: BMC Genomics 2013 14:201
    Content type: Research article Published on:

  47. The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and...

    Authors: Søren F Schmidt, Mette Jørgensen, Yun Chen, Ronni Nielsen, Albin Sandelin and Susanne Mandrup
    Citation: BMC Genomics 2011 12:152
    Content type: Research article Published on:

  48. Genome-wide expression profiles reflect the transcriptional networks specific to the given cell context. However, most statistical models try to estimate the average connectivity of the networks from a collect...

    Authors: Sang-Mun Chi, Young-Kyo Seo, Young-Kyu Park, Sora Yoon, Chan Young Park, Yong Sung Kim, Seon-Young Kim and Dougu Nam
    Citation: BMC Genomics 2014 15:450
    Content type: Methodology article Published on:

  50. Trypanosomatids are a group of protozoan parasites that includes the etiologic agents of important human illnesses as Chagas disease, sleeping sickness and leishmaniasis. These parasites have a significant dis...

    Authors: Rafael Luis Kessler, Daniela Parada Pavoni, Marco Aurelio Krieger and Christian Macagnan Probst
    Citation: BMC Genomics 2017 18:793
    Content type: Methodology article Published on:

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