[PDF] Top 20 A systems biology approach to transcription factor binding site prediction.
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A systems biology approach to transcription factor binding site prediction.
... used to infer regulatory interactions between TFs and their targets [16,31,32,33], but co- expression alone is not sufficient for determining direct interac- ...attempt to use additional properties of the ... See full document
10
DNA-MATRIX: a tool for constructing transcription factor binding sites Weight matrix
... TF binding sites prediction in whole genome remains a challenge for the researchers because of the Chemistery of genomic-DNA interaction is poorly ...heuristic approach for weight matrix ... See full document
3
Prediction of nucleosome positioning based on transcription factor binding sites.
... coded to a vector with 35 dimensions, with each dimension representing one family of TFBS ...possible to evaluate the importance of each TFBS family in the formation or inhibition of nucleosome positioning ... See full document
7
Systems Biology Approach to Study the High Altitude Adaptation in Tibetans
... a transcription factor regulating the gene expression in response to the hypoxia (Tian et ...addition to the hypoxic response function, the EGLN1 is being considered as an important ... See full document
8
The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs.
... matching approach we found the CArG-box in 1,063 (approximately 80%) Srf binding ...second binding event of the studied factors occurred at sequence sites containing at least two times the respective ... See full document
16
A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells.
... subsets. To initially characterise the 2 subnetworks, Pathway (from Reactome) and GO term over-representation analysis was performed on the genes comprising the ...relating to TLR4 signalling, including ... See full document
16
Transcription factor binding sites prediction based on modified nucleosomes.
... for transcription factor binding site (TFBS) ...sequences to predict actual binding sites, they usually produce a large number of false positive (FP) predictions and so are ... See full document
10
A structural-based strategy for recognition of transcription factor binding sites.
... functions to the prediction of TFBS sites, we were motivated to explore other modifications that could improve the performance of vcFIRE in this ...modifications to the existing ... See full document
10
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.
... shown to perform better than general purpose sequence alignment ...each transcription factor (except Gt and Kni, see Materials and Methods), as per ChIP-chip assays in Li et ...close to ... See full document
14
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.
... compared to the number of TFs. They try to generalize the properties of the already known TFBMs to find new ...of binding sites targeted by TFBMs is very small compared to the number of ... See full document
13
A linear model for transcription factor binding affinity prediction in protein binding microarrays.
... from binding-enriched unaligned sequenc- ...model-based approach and develop a Gibbs sampling technique for statistical inference ...(EM) to simultaneously align sequences and discover contiguous PWM ... See full document
13
Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.
... their binding sites must have enough information to be distinguishable from all other sequences in the genome, and (2) they must bind these sites with an affinity that appropriately modulates the rate of ... See full document
13
Nonidentifiability of the source of intrinsic noise in gene expression from single-burst data.
... of transcription factor, RNA polymerase, ribosome and RNase binding leads to what is now widely regarded as the standard model of gene expression for prokaryotes ...theorem to obtain ... See full document
10
Clustering Approach to Stock Market Prediction
... 2000) to achieve our ...stocks to k different groups represented by the ...perhaps to choose the ‘right’ k corresponding to the natural number of clusters in the ...methods to verify ... See full document
11
Pathogenomic inference of virulence-associated genes in Leptospira interrogans.
... responses to infection ...known to mediate protein-protein interactions and have recently been recognized as components of bacterial virulence mechanisms ...homology to a toxin (NCBI protein cluster ... See full document
11
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
... previous binding site prediction algorithms have considered both sequence and ...the prediction of functional surface patches from ...found to overlap with functional sites [41], and ... See full document
18
Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.
... The site of acetylation, Lys180, appears to be critical for RcsB DNA-binding activity, as evidenced by a lack of shift in the mobility of the flhDC probe when incubated with RcsB carrying acetylation ... See full document
9
Stem cells living with a Notch
... contrast to the wealth of supportive data obtained by Notch gain-of-function analysis, several genetic studies using loss-of- function approaches have not identified an essential role for Notch signaling in adult ... See full document
16
Genética molecular aplicada ao câncer cutâneo não melanoma.
... Enquanto os proto-oncogenes promovem o crescimento celular, existe uma classe de genes, denominados genes supressores de tumor, que atua inibindo o ciclo de divisão das células. Ao contrário dos oncogenes, que podem ... See full document
15
Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.
... shown to bind to AC elements and activate transcription in yeast and in planta; however, these studies did not correlate binding affinity with ability to activate transcription ... See full document
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