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

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  1. Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially b...

    Authors: Ximiao He, Raghunath Chatterjee, Sam John, Hector Bravo, B K Sathyanarayana, Simon C Biddie, Peter C FitzGerald, John A Stamatoyannopoulos, Gordon L Hager and Charles Vinson
    Citation: BMC Genomics 2013 14:428
    Content type: Research article Published on:

  2. Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour...

    Authors: Darrell Lizamore, Ross Bicknell and Chris Winefield
    Citation: BMC Genomics 2021 22:676
    Content type: Research article Published on:

  3. The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate le...

    Authors: Silvia Picossi, Enrique Flores and Antonia Herrero
    Citation: BMC Genomics 2014 15:22
    Content type: Research article Published on:

  4. Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the u...

    Authors: Kate Keogh, D. A. Kenny, P. A. Alexandre, M. McGee and A. Reverter
    Citation: BMC Genomics 2024 25:234
    Content type: Research Published on:

  5. Prior work demonstrated that female rats (but not their male littermates) exposed to methamphetamine become hypersensitive to myocardial ischemic injury. Importantly, this sex-dependent effect persists followi...

    Authors: Hasitha Chavva, Daniel A. Brazeau, James Denvir, Donald A. Primerano, Jun Fan, Sarah L. Seeley and Boyd R. Rorabaugh
    Citation: BMC Genomics 2021 22:259
    Content type: Research article Published on:

  6. Heat shock transcriptional factors (Hsfs) play important roles in the processes of biotic and abiotic stresses as well as in plant development. Cotton (Gossypium hirsutum, 2n = 4x = (AD)2 = 52) is an important cr...

    Authors: Jun Wang, Na Sun, Ting Deng, Lida Zhang and Kaijing Zuo
    Citation: BMC Genomics 2014 15:961
    Content type: Research article Published on:

  7. Multiplex experimental assays coupled to computational predictions are being increasingly employed for the simultaneous analysis of many specimens at the genome scale, which quickly generates very large amount...

    Authors: Milos Pjanic, Petar Pjanic, Christoph Schmid, Giovanna Ambrosini, Armelle Gaussin, Genta Plasari, Christian Mazza, Philipp Bucher and Nicolas Mermod
    Citation: BMC Genomics 2011 12:181
    Content type: Research article Published on:

  8. Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms ...

    Authors: Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang and Yuhua Wang
    Citation: BMC Genomics 2016 17:809
    Content type: Research article Published on:

  9. The AP2/ERF transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses. Although...

    Authors: Licao Cui, Kewei Feng, Mengxing Wang, Meng Wang, Pingchuan Deng, Weining Song and Xiaojun Nie
    Citation: BMC Genomics 2016 17:636
    Content type: Research article Published on:

  10. Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main trans...

    Authors: Wei Li, Ziwen Geng, Cuiping Zhang, Kuiling Wang and Xinqiang Jiang
    Citation: BMC Genomics 2021 22:90
    Content type: Research article Published on:

  11. Walnut (Juglans regia) is an important tree cultivated worldwide and is exposed to a series of both abiotic and biotic stress during their life-cycles. The heat stress transcription factors (HSFs) play a crucial ...

    Authors: Xuejiao Liu, Panpan Meng, Guiyan Yang, Mengyan Zhang, Shaobing Peng and Mei Zhi Zhai
    Citation: BMC Genomics 2020 21:474
    Content type: Research article Published on:

  12. Transcription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However...

    Authors: Qi Yan, Fan Wu, Tiantian Ma, Xifang Zong, Qian Ma, Jie Li, Yufeng Zhao, Yanrong Wang and Jiyu Zhang
    Citation: BMC Genomics 2019 20:760
    Content type: Research article Published on:

  13. The molecular mechanisms underlying the sex differences in human muscle morphology and function remain to be elucidated. The sex differences in the skeletal muscle transcriptome in both the resting state and f...

    Authors: Dongmei Liu, Maureen A Sartor, Gustavo A Nader, Laurie Gutmann, Mary K Treutelaar, Emidio E Pistilli, Heidi B IglayReger, Charles F Burant, Eric P Hoffman and Paul M Gordon
    Citation: BMC Genomics 2010 11:659
    Content type: Research article Published on:

  14. Dysregulation of the common stress responsive transcription factor ATF3 has been causally linked to many important human diseases such as cancer, atherosclerosis, infections, and hypospadias. Although it is be...

    Authors: Jonathan Zhao, Xingyao Li, Mingxiong Guo, Jindan Yu and Chunhong Yan
    Citation: BMC Genomics 2016 17:335
    Content type: Research article Published on:

  15. Variability in protein levels is generated through intricate control of the different gene decoding phases. Presently little is known about the links between the various gene expression stages. Here we investi...

    Authors: Ana Tamarkin-Ben-Harush, Edna Schechtman and Rivka Dikstein
    Citation: BMC Genomics 2014 15:688
    Content type: Research article Published on:

  17. Grapevine (Vitis species) is among the most important fruit crops in terms of cultivated area and economic impact. Despite this relevance, little is known about the transcriptional changes and the regulatory circ...

    Authors: Stefania Pilati, Michele Perazzolli, Andrea Malossini, Alessandro Cestaro, Lorenzo Demattè, Paolo Fontana, Antonio Dal Ri, Roberto Viola, Riccardo Velasco and Claudio Moser
    Citation: BMC Genomics 2007 8:428
    Content type: Research article Published on:

  18. The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and trans...

    Authors: Diana L Williams, Richard A Slayden, Amol Amin, Alejandra N Martinez, Tana L Pittman, Alex Mira, Anirban Mitra, Valakunja Nagaraja, Norman E Morrison, Milton Moraes and Thomas P Gillis
    Citation: BMC Genomics 2009 10:397
    Content type: Research article Published on:

  19. Effects on gene expression due to environmental or genetic changes can be easily measured using microarrays. However, indirect effects on expression can be substantial. The indirect effects of a perturbation n...

    Authors: Lin Tang, Xiao Liu and Neil D Clarke
    Citation: BMC Genomics 2006 7:215
    Content type: Research article Published on:

  20. Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly being applied to study transcriptional regulation on a genome-wide scale. While numerous algorithms have rece...

    Authors: Teemu D Laajala, Sunil Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio and Laura L Elo
    Citation: BMC Genomics 2009 10:618
    Content type: Research article Published on:

  21. Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stre...

    Authors: Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lianxue Fan and Liwang Liu
    Citation: BMC Genomics 2019 20:772
    Content type: Research article Published on:

  22. Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that is widely found in plants and animals, and is the second largest transcription factor family in eukaryotes after MYB. They have been...

    Authors: Yu Fan, Hao Yang, Dili Lai, Ailing He, Guoxing Xue, Liang Feng, Long Chen, Xiao-bin Cheng, Jingjun Ruan, Jun Yan and Jianping Cheng
    Citation: BMC Genomics 2021 22:415
    Content type: Research Published on:

  23. Squamous promoter binding protein-like (SPL) proteins are a class of transcription factors that play essential roles in plant growth and development, signal transduction, and responses to biotic and abiotic st...

    Authors: Yanyan Ren, Rui Ma, Yue Fan, Bingjie Zhao, Peng Cheng, Yu Fan and Baotong Wang
    Citation: BMC Genomics 2022 23:773
    Content type: Research Published on:

  24. GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, indu...

    Authors: Yao Chen, Panpan Zhu, Shaoyuan Wu, Yan Lu, Jian Sun, Qinghe Cao, Zongyun Li and Tao Xu
    Citation: BMC Genomics 2019 20:911
    Content type: Research article Published on:

  25. Transcription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism. The identificat...

    Authors: Niharika Sharma, Prem L Bhalla and Mohan B Singh
    Citation: BMC Genomics 2013 14:915
    Content type: Research article Published on:

  26. Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the...

    Authors: Qi Liu, Russell Bonneville, Tianbao Li and Victor X. Jin
    Citation: BMC Genomics 2017 18:375
    Content type: Methodology article Published on:

  27. In eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relative...

    Authors: Evelien M Bunnik, Anton Polishko, Jacques Prudhomme, Nadia Ponts, Sarjeet S Gill, Stefano Lonardi and Karine G Le Roch
    Citation: BMC Genomics 2014 15:347
    Content type: Research article Published on:

  28. Prostate cancer is one of the leading causes of cancer death in men. Androgen ablation, the most commonly-used therapy for progressive prostate cancer, is ineffective once the cancer cells become androgen-inde...

    Authors: Guohua Wang, Yadong Wang, Weixing Feng, Xin Wang, Jack Y Yang, Yuming Zhao, Yue Wang and Yunlong Liu
    Citation: BMC Genomics 2008 9(Suppl 2):S22
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  29. Fusarium oxysporum f. sp. cucumerinum (FOC) is the causal agent of cucumber Fusarium wilt, which can cause extensive damages and productivity losses. Cucurbita ficifolia Bouché (Cucurbitaceae) is usually used as ...

    Authors: Junjun Xie, Yumei Ding, Ting Gao, Shuilian He, Kai Zhao, Xuehu Yang, Jie Zhang and Zhengan Yang
    Citation: BMC Genomics 2022 23(Suppl 1):436
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  30. Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing ...

    Authors: Guan-Dong Shang, Zhou-Geng Xu, Mu-Chun Wan, Fu-Xiang Wang and Jia-Wei Wang
    Citation: BMC Genomics 2022 23(Suppl 1):272
    Content type: Software Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  31. The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four...

    Authors: Amit Katiyar, Shuchi Smita, Sangram Keshari Lenka, Ravi Rajwanshi, Viswanathan Chinnusamy and Kailash Chander Bansal
    Citation: BMC Genomics 2012 13:544
    Content type: Research article Published on:

  32. The MYB superfamily is one of the most abundant transcription factor (TF) families in plants. MYB proteins include highly conserved N-terminal MYB repeats (1R, R2R3, 3R, and atypical) and various C-terminal se...

    Authors: Zhen Wang, Jun Tang, Rong Hu, Peng Wu, Xi-Lin Hou, Xiao-Ming Song and Ai-Sheng Xiong
    Citation: BMC Genomics 2015 16:17
    Content type: Research article Published on:

  33. The balance between endothelial cell survival and apoptosis during stress is an important cellular process for vessel integrity and vascular homeostasis, and it is also pivotal in angiogenesis during the devel...

    Authors: Xingyi Hang, Peiyao Li, Zhifeng Li, Wubin Qu, Ying Yu, Hualing Li, Zhiyong Shen, Hao Zheng, Yan Gao, Yonghong Wu, Minghua Deng, Zhixian Sun and Chenggang Zhang
    Citation: BMC Genomics 2009 10:126
    Content type: Research article Published on:

  35. Changes in cellular phenotype result from underlying changes in mRNA transcription and translation. Endothelin-1 stimulates cardiomyocyte hypertrophy with associated changes in mRNA/protein expression and an i...

    Authors: Thomais Markou, Andrew K Marshall, Timothy E Cullingford, El L Tham, Peter H Sugden and Angela Clerk
    Citation: BMC Genomics 2010 11:343
    Content type: Research article Published on:

  36. MicroRNAs (miRNAs) play a fundamental role in the regulation of gene expression by translational repression or target mRNA degradation. Regulatory elements in miRNA promoters are less well studied, but may rev...

    Authors: Bastiaan JH Jansen, Iziah E Sama, Dagmar Eleveld-Trancikova, Maaike A van Hout-Kuijer, Joop H Jansen, Martijn A Huynen and Gosse J Adema
    Citation: BMC Genomics 2011 12:330
    Content type: Research article Published on:

  37. Trypanosomatids utilise polycistronic transcription for production of the vast majority of protein-coding mRNAs, which operates in the absence of gene-specific promoters. Resolution of nascent transcripts by p...

    Authors: V Lila Koumandou, Senthil Kumar A Natesan, Tatiana Sergeenko and Mark C Field
    Citation: BMC Genomics 2008 9:298
    Content type: Research article Published on:

  38. Tuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is u...

    Authors: Zhaoqin Cai, Zhipeng Cai, Jingli Huang, Aiqin Wang, Aaron Ntambiyukuri, Bimei Chen, Ganghui Zheng, Huifeng Li, Yongmei Huang, Jie Zhan, Dong Xiao and Longfei He
    Citation: BMC Genomics 2022 23:473
    Content type: Research Published on:

  39. Heat shock response in eukaryotes is transcriptionally regulated by conserved heat shock transcription factors (Hsfs). Hsf genes are represented by a large multigene family in plants and investigation of the H...

    Authors: Yong-Xiang Lin, Hai-Yang Jiang, Zhang-Xin Chu, Xiu-Li Tang, Su-Wen Zhu and Bei-Jiu Cheng
    Citation: BMC Genomics 2011 12:76
    Content type: Research article Published on:

  40. Wucai suffers from low temperature during the growth period, resulting in a decline in yield and poor quality. But the molecular mechanisms of cold tolerance in wucai are still unclear.

    Authors: Chenggang Wang, Mengyun Zhang, Jiajie Zhou, Xun Gao, Shidong Zhu, Lingyun Yuan, Xilin Hou, Tongkun Liu, Guohu Chen, Xiaoyan Tang, Guolei Shan and Jinfeng Hou
    Citation: BMC Genomics 2022 23:137
    Content type: Research Published on:

  41. Mitochondrial transcription termination factor (mTERF) is a large gene family which plays a significant role during plant growth under various environmental stresses. However, knowledge of mTERF genes in grape...

    Authors: Xiangjing Yin, Yu Gao, Shiren Song, Danial Hassani and Jiang Lu
    Citation: BMC Genomics 2021 22:136
    Content type: Research article Published on:

  42. Chinese kale (Brassica alboglabra) contains high nutritional elements and functional molecules, especially anticarcinogenic and antioxidant glucosinolates (GS), which was highly affected by environment temperatur...

    Authors: Rongfang Guo, Xingru Wang, Xiaoyun Han, Wenjing Li, Tao Liu, Bingxing Chen, Xiaodong Chen and Gefu Wang-Pruski
    Citation: BMC Genomics 2019 20:269
    Content type: Research article Published on:

  43. Ultraconserved elements (UCEs) are highly constrained elements of mammalian genomes, whose functional role has not been completely elucidated yet. Previous studies have shown that some of them act as enhancers...

    Authors: Danilo Licastro, Vincenzo A Gennarino, Francesca Petrera, Remo Sanges, Sandro Banfi and Elia Stupka
    Citation: BMC Genomics 2010 11:151
    Content type: Research article Published on:

  44. This is a first report, using our MotifModeler informatics program, to simultaneously identify transcription factor (TF) and microRNA (miRNA) binding sites from gene expression microarray data. Based on the assum...

    Authors: Guohua Wang, Xin Wang, Yadong Wang, Jack Y Yang, Lang Li, Kenneth P Nephew, Howard J Edenberg, Feng C Zhou and Yunlong Liu
    Citation: BMC Genomics 2008 9(Suppl 1):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  45. Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily ...

    Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, Jill L. Wegrzyn, David B. Neale, J. Bradley St. Clair and Dee R. Denver
    Citation: BMC Genomics 2017 18:558
    Content type: Research article Published on:

  46. Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which lea...

    Authors: Renan Terassi Pinto, Natália Chagas Freitas, Wesley Pires Flausino Máximo, Thiago Bergamo Cardoso, Débora de Oliveira Prudente and Luciano Vilela Paiva
    Citation: BMC Genomics 2019 20:812
    Content type: Research article Published on:

  47. Echinococcus granulosus sensu lato has a complex developmental biology with a variety of factors relating to both intermediate and final hosts. To achieve maximum parasite adaptability, the development of the ces...

    Authors: Mohammad Ali Mohammadi, Mehdi Mansouri, Ali Derakhshani, Masoud Rezaie, Mehdi Borhani, Saeid Nasibi, Seyed Mohammad Mousavi, Ali Afgar, Natalia Macchiaroli, Mara C. Rosenzvit and Majid Fasihi Harandi
    Citation: BMC Genomics 2023 24:114
    Content type: Research Published on:

  48. Acer pseudosieboldianum is a kind of excellent color-leafed plants, and well known for its red leaves in autumn. At the same time, A. pseudosieboldianum is one of the native tree species in the northeast of China...

    Authors: Jia-Lin Li, Zhuo Weng, Xin-Yu Li, Bo Xu, Yu-Fu Gao and Li-Ping Rong
    Citation: BMC Genomics 2022 23:567
    Content type: Research Published on:

  49. Blueberry (Vaccinium corymbosum L.) is an important species with a high content of flavonoids in fruits. As a perennial shrub, blueberry is characterized by shallow-rooted property and susceptible to drought stre...

    Authors: Aibin Wang, Kehao Liang, Shiwen Yang, Yibo Cao, Lei Wang, Ming Zhang, Jing Zhou and Lingyun Zhang
    Citation: BMC Genomics 2021 22:565
    Content type: Research article Published on:

  50. Whole genome sequencing provides the most comprehensive collection of an organism’s genetic information. The availability of complete genome sequences is expected to dramatically deliver a high impact on biolo...

    Authors: Chenglin Chai, Yongqin Wang, Trupti Joshi, Babu Valliyodan, Silvas Prince, Lydia Michel, Dong Xu and Henry T. Nguyen
    Citation: BMC Genomics 2015 16:596
    Content type: Research article Published on:

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