Transcriptional Networks
Identification of hoxb1b downstream genes: hoxb1b as a regulatory factor controlling transcriptional networks and cell movement during zebrafish gastrulation
... ABSTRACT Hox proteins are homeobox containing transcription factors that play important roles in patterning the presumptive central nervous system and the axial mesoderm in the early vertebrate embryo. Hox genes are ...
9
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
... Gene function and phylogenetic conservation were found to be related constraints on gene positioning at the whole genome level in Fusarium. Rates of recombin- ation were associated with levels of protein sequence ...
17
Genetic risk for Alzheimer’s disease is concentrated in specific macrophage and microglial transcriptional networks
... Although GWAS have identified thousands of variants that influence diseases and traits, the majority are located in non-coding regions of the genome [2]. Com- bined with small effect sizes, the biological interpretation ...
10
Responses of Pathogenic and Nonpathogenic Yeast Species to Steroids Reveal the Functioning and Evolution of Multidrug Resistance Transcriptional Networks
... PDR networks by directly modifying the activity and properties of some PDR ABC ...PDR transcriptional networks and thus the PDR status of yeast ...
10
Modelling transcriptional networks in plant senescence
... The remaining six clusters are all related to the function of photosynthesis it- self and, together, these over-represented GO terms account for 72 genes. The most interesting aspect of these genes is that they are all ...
371
Mapping Yeast Transcriptional Networks
... The Polymerase A and C (PAC) and RRPE motifs are a particularly striking example of both the success and the frustration that can be associated with motif discovery. The PAC motif was first found in 1991 by manual ...
28
Genomic analysis of transcriptional networks directing progression of cell states during MGE development
... Technical advancements in genome wide sequencing, chromosome capture and CRISPR/Cas9 technologies are increasing our understanding of genome organization. These data, combined with data showing RE activities in vivo ...
12
FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch.
... Since singing-driven gene coexpression patterns were similar between juvenile and adult Area X, the capacity to learn vocalizations is not a product of large-scale differences in coexpression of the song production ...
36
Correlating transcriptional networks to breast cancer survival: a large scale coexpression analysis
... Once again, individual probesets within this module follow a similar pattern to that of the coexpression cluster, for instance, CD53 had significant associations with good prognosis for [r] ...
9
Evaluating the Effects of Increasing Nighttime Temperature on the Circadian Clock using Transcriptional Networks.
... HNT poses an interesting problem because their effects can be thought of in two different manners: 1) HNT affects the thermocycles that help daily coordinate activities, and the loss of this signal can impact plant ...
175
Modular Transcriptional Networks of the Host Pulmonary Response during Early and Late Pneumococcal Pneumonia
... such networks has been highlighted by evidence of bac- terial virulence factors directly targeting network hub components to suppress the hosts’ immune response ...
12
CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment
... Next, we compared the lists of DEGs in CHD8 +/− NPCs and neurons with genes previously associated with brain size or volumes of specific brain regions. Recent GWASs revealed a small number of common variants associated ...
18
Dissecting the transcriptional networks underlying breast cancer: NR4A1 reduces the migration of normal and breast cancer cell lines
... To determine whether the ability of NR4A1 to reduce migration is specific to the MCF-10A cells, another normal mammary epithelial cell line 226L ectopically expressing NR4A1 Figure 4a wa[r] ...
17
MECoRank: cancer driver genes discovery simultaneously evaluating the impact of SNVs and differential expression on transcriptional networks
... stabilization by directly targeting YWHAG [25]. And ATXN1 is the target of miR-221 in regulating normal and malignant breast stem-like cells [26]. This is one of the few reports about ATXN1’s role in breast cancer. And ...
10
Abundance of connected motifs in transcriptional networks, a case study using random forests regression
... In order to understand the features contributing to higher network robustness, we studied several network character- istics. While some of these characteristics such as average shortest path, network density, and ...
8
Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
... AUC: area under the curve; ChIP: chromatin immunoprecipitation; ChIP- seq: ChIP followed by next generation sequencing; DMR: differentially methylated region; GSEA: gene set enrichment a[r] ...
15
Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks
... the networks constructed by selecting appropriate subsets of these ...the networks correspond to specific combinations of positive and negative correlation values (Figure ...
17
Dysregulated transcriptional networks in KMT2A- and MLLT10-rearranged T-ALL
... biological networks with MLLT10 -R [4], KMT2A -R also shared similar gene expression signatures with KMT2A -R in AML or BCP-ALL [5, 11, ...signaling networks that could discriminate be- tween KMT2A -R and ...
6
In vitro synthetic transcriptional networks
... logical networks with increasing complexity and offer a testbed for probing the design space of biochemical ...implementing networks of arbitrary complexity (Hopfield ...vitro transcriptional cir- ...
118
Toward understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice
... tory networks in ...by transcriptional networks, and focus on TFs that function in abiotic stress responses and confer stress tolerance in ...
9