2,863 research outputs found
HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions
Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).
Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.
Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes
The Likelihood Ratio Test and Full Bayesian Significance Test under small sample sizes for contingency tables
Hypothesis testing in contingency tables is usually based on asymptotic
results, thereby restricting its proper use to large samples. To study these
tests in small samples, we consider the likelihood ratio test and define an
accurate index, the P-value, for the celebrated hypotheses of homogeneity,
independence, and Hardy-Weinberg equilibrium. The aim is to understand the use
of the asymptotic results of the frequentist Likelihood Ratio Test and the
Bayesian FBST -- Full Bayesian Significance Test -- under small-sample
scenarios. The proposed exact P-value is used as a benchmark to understand the
other indices. We perform analysis in different scenarios, considering
different sample sizes and different table dimensions. The exact Fisher test
for tables that drastically reduces the sample space is also
discussed. The main message of this paper is that all indices have very similar
behavior, so the tests based on asymptotic results are very good to be used in
any circumstance, even with small sample sizes
Strong superadditivity and monogamy of the Renyi measure of entanglement
Employing the quantum R\'enyi -entropies as a measure of
entanglement, we numerically find the violation of the strong superadditivity
inequality for a system composed of four qubits and . This violation
gets smaller as and vanishes for when the
measure corresponds to the Entanglement of Formation (EoF). We show that the
R\'enyi measure aways satisfies the standard monogamy of entanglement for
, and only violates a high order monogamy inequality, in the rare
cases in which the strong superadditivity is also violated. The sates
numerically found where the violation occurs have special symmetries where both
inequalities are equivalent. We also show that every measure satisfing monogamy
for high dimensional systems also satisfies the strong superadditivity
inequality. For the case of R\'enyi measure, we provide strong numerical
evidences that these two properties are equivalent.Comment: replaced with final published versio
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