Abstract:
:Defects in the initial establishment of cardiogenic cell fate are likely to contribute to pervasive human congenital cardiac abnormalities. However, the molecular underpinnings of nascent cardiac fate induction have proven difficult to decipher. In this review we explore the participation of extracellular, cellular and nuclear factors in comprehensive specification networks. At each level, we elaborate on insights gained through the study of cardiogenesis in the invertebrate chordate Ciona intestinalis and propose productive lines of future research. In-depth discussion of pre-cardiac induction is intended to serve as a paradigm, illustrating the potential use of Ciona to elucidate comprehensive networks underlying additional aspects of chordate cardiogenesis, including directed migration and subspecification of cardiac and pharyngeal lineages.
journal_name
Brief Funct Genomicsjournal_title
Briefings in functional genomicsauthors
Cota CD,Segade F,Davidson Bdoi
10.1093/bfgp/elt034subject
Has Abstractpub_date
2014-01-01 00:00:00pages
3-14issue
1eissn
2041-2649issn
2041-2657pii
elt034journal_volume
13pub_type
杂志文章,评审abstract::Omics, such as genomics, transcriptome and proteomics, has been affected by the era of big data. A huge amount of high dimensional and complex structured data has made it no longer applicable for conventional machine learning algorithms. Fortunately, deep learning technology can contribute toward resolving these chall...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/ely030
更新日期:2019-02-14 00:00:00
abstract::DNA methylation is an epigenetic modification of cytosines that undergoes dynamic changes in a temporal, spatial and cell-type-specific manner. Recent advances in technology have permitted the profiling of high-throughput methylomes in large numbers of biological samples. Various computational tools have been develope...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw029
更新日期:2016-11-01 00:00:00
abstract::Gastric cancer remains the second most common cause of cancer-related death worldwide. Because of the poor prognosis of late-stage gastric cancer patients, it is imperative to develop new strategies to improve the survival rate of this disease. Currently, immunotherapy is considered as an innovative approach for cance...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/ely019
更新日期:2019-03-22 00:00:00
abstract::Less than 2% of the human genome DNA is composed of protein-coding genes, although the majority of the human genome is transcribed, indicating the transcripts mostly are noncoding RNAs. Those noncoding RNAs with length between 200 nt and 200 kb are categorized as long noncoding RNA (lncRNA). Around 30 000 lncRNAs have...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv049
更新日期:2016-05-01 00:00:00
abstract::Molecular network data are increasingly becoming available, necessitating the development of well performing computational tools for their analyses. Such tools enabled conceptually different approaches for exploring human diseases to be undertaken, in particular, those that study the relationship between a multitude o...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/els037
更新日期:2012-11-01 00:00:00
abstract::Genetic variation is crucial for successful barley improvement. Genomic technologies are improving dramatically and are providing access to the genetic diversity within this important crop species. Diverse collections of barley germplasm are being assembled and mined via genome-wide association studies and the identif...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elu006
更新日期:2014-07-01 00:00:00
abstract::Next generation Sequencing (NGS) provides a powerful tool for discovery of domestication genes in crop plants and their wild relatives. The accelerated domestication of new plant species as crops may be facilitated by this knowledge. Re-sequencing of domesticated genotypes can identify regions of low diversity associa...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
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更新日期:2012-01-01 00:00:00
abstract::The human genome has an almost equal distribution of unique and transposable genetic elements. Although at the transcriptome level, a relatively higher contribution from transposable elements derived RNA has been reported. This is further highlighted with evidence from pervasive transcription. Of the total RNA, noncod...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elaa026
更新日期:2021-01-25 00:00:00
abstract::Piwi-interacting RNAs (piRNAs) and CRISPR RNAs (crRNAs) are two recently discovered classes of small noncoding RNA that are found in animals and prokaryotes, respectively. Both of these novel RNA species function as components of adaptive immune systems that protect their hosts from foreign nucleic acids-piRNAs repres...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
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更新日期:2012-07-01 00:00:00
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journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elz037
更新日期:2020-01-22 00:00:00
abstract::The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein-protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae In particula...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv040
更新日期:2016-03-01 00:00:00
abstract::A recent highlight of genomics research has been the discovery of many families of transcripts which have function but do not code for proteins. An important group is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. We review prog...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elu017
更新日期:2015-03-01 00:00:00
abstract::High-throughput next-generation sequencing (NGS) technologies have rapidly generated a large volume of genomic data. To aid the development and evaluation of new statistical models and computational methods, NGS-based simulators have been proposed to construct better experimental workflows. However, the comparative pe...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw012
更新日期:2017-05-01 00:00:00
abstract::Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding R...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elx018
更新日期:2018-01-01 00:00:00
abstract::Premature termination of transcription, or attenuation, is an efficient RNA-based regulatory strategy that is commonly used in bacterial organisms. Attenuators are generally located in the 50 untranslated regions of genes or operons and combine a Rho-independent terminator, controlling transcription, with an RNA eleme...
journal_title:Briefings in functional genomics
pub_type: 更正并重新发布的文章,杂志文章,评审
doi:10.1093/bfgp/elq008
更新日期:2010-03-01 00:00:00
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journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/ely007
更新日期:2018-09-27 00:00:00
abstract::The polycomb group (PcG) proteins are key epigenetic regulators of gene expression in animals and plants. They act in multiprotein complexes, of which the best characterized is the polycomb repressive complex 2 (PRC2), which catalyses the trimethylation of histone H3 at lysine 27 (H3K27me3) at chromatin targets. In Ar...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elw007
更新日期:2017-03-01 00:00:00
abstract::The growing appreciation of the importance of long noncoding RNAs (lncRNAs), together with the awareness that some of these RNAs are associated with chromatin, has inspired the development of methods to detect their sites of interaction on a genome-wide scale at high resolution. Hybridization capture methods combine a...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elx038
更新日期:2018-03-01 00:00:00
abstract::Neisseria meningitidis is a strictly human pathogen and is one of the major causes of septicemia and meningitis worldwide. Functional genomics approaches have been extensively applied to study how N. meningitidis adapts to grow and survive in different human niches encountered during the infection. DNA microarrays per...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elt018
更新日期:2013-07-01 00:00:00
abstract::Chronic infection of hepatitis C virus (HCV) leads to severe life-threatening liver diseases such as cirrhosis of liver, fibrosis and hepatocellular carcinoma (HCC). Severity of the disease infects >180 million people worldwide. In recent years, many computational approaches have been proposed to study and analyze the...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elx040
更新日期:2018-11-26 00:00:00
abstract::Epigenetic memory represents a natural mechanism whereby the identity of a cell is maintained through successive cell cycles, allowing the specification and maintenance of differentiation during development and in adult cells. Cancer is a loss or reversal of the stable differentiated state of adult cells and may be me...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt011
更新日期:2013-05-01 00:00:00
abstract::Aberrant DNA methylation is considered to be one of the most common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNA methylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw010
更新日期:2016-11-01 00:00:00
abstract::Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize th...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv002
更新日期:2015-11-01 00:00:00
abstract::The Notch signalling pathway plays crucial roles in cardiac development and postnatal cardiac homoeostasis. Gain- and loss-of-function approaches indicate that Notch promotes or inhibits cardiogenesis in a stage-dependent manner. However, the molecular mechanisms are poorly defined because many downstream effectors re...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt036
更新日期:2014-01-01 00:00:00
abstract::Coronary artery disease (CAD) and ischemic stroke are the two most predominant forms of cardiovascular diseases (CVDs) caused by genetic, epigenetic and environmental risk factors. Although studies on the impact of 'epigenetics' in CVDs is not new, its effects are increasingly being realized as a key regulatory determ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elz043
更新日期:2020-07-29 00:00:00
abstract::The epitome of any genome research is to identify all the existing genes in a genome and investigate their roles. Various techniques have been applied to unveil the functions either by silencing or over-expressing the genes by targeted expression or random mutagenesis. Rice is the most appropriate model crop for gener...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elw041
更新日期:2017-07-01 00:00:00
abstract::Lysine N-ε-acetylation is a post-translational modification that regulates the function of histone and non-histone proteins. In several malignancies, histone acetyltransferase (HAT) activities are disturbed as a consequence of various genetic or epigenetic alterations. In particular, HATs can function as tumor suppres...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/els065
更新日期:2013-05-01 00:00:00
abstract::Pluripotent embryonic stem (ES) cells are specialized cells with a dynamic chromatin structure, which is intimately connected with their pluripotency and physiology. In recent years somatic cells have been reprogrammed to a pluripotent state through over-expression of a defined set of transcription factors. These cell...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elq038
更新日期:2011-01-01 00:00:00
abstract::Recent data have revealed that the paradigmatic tumour suppressor gene RB1 on chromosome 13 is preferentially expressed from the maternal allele. Imprinted expression of RB1 is linked to a differentially methylated CpG island in intron 2 of this gene (CpG 85). On the paternal chromosome, CpG 85 is unmethylated and act...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elq014
更新日期:2010-07-01 00:00:00
abstract::In order to better understand several cellular processes, it is helpful to study how various components make up the system. This systems perspective is supported by several modelling tools including network analysis. Networks of protein-protein interactions (PPI networks) offer a way to depict, visualize and quantify ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/els035
更新日期:2012-11-01 00:00:00