UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks

Kalathur, Ravi Kiran Reddy; Pinto, José; Hernández‐Prieto, Miguel A.; Machado, Rui S. R.; Almeida, Dulce Maria Gomes de; Chaurasia, Gautam; Futschik, Matthias E.

doi:10.1093/nar/gkt1100

Cited by 83 publications

(43 citation statements)

References 49 publications

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“…They also demonstrated ACSS2 is specifically expressed in mouse facial tissue during development. ACSS2 interacts with several genes previously identified by Jugessur et al as genes possibly related to clefting: ALDH1A1, ATIC, CTH, DARS, MTHFD1, CBS, and LPL [Jugessur et al, 2009;Kalathur et al, 2013]. PHYH has been associated with rhizomelic chondrodysplasia punctata, which can include craniofacial anomalies such as micrognathia and high arched palate [Barr et al, 1993;Jansen et al, 1997] PHYH has been shown to interact with PEX7, a previously identified gene possibly linked to clefting [Jugessur et al, 2009;Kalathur et al, 2013].…”

Section: Discussionmentioning

confidence: 97%

Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate

Aylward

Cai

Lee

et al. 2016

Genetic Epidemiology

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INTRODUCTION Studies suggest that nonsyndromic cleft lip and palate (NSCLP) is polygenic with variable penetrance, presenting a challenge in identifying all causal genetic variants. Despite relatively high prevalence of NSCLP among Amerindian populations, no large whole exome sequencing (WES) studies have been completed in this population. OBJECTIVE Identify candidate genes with rare genetic variants for NSCLP in a Honduran population using WES. METHODS WES was performed on two to four members of 27 multiplex Honduran families. Genetic variants with a minor allele frequency > 1% in reference databases were removed. Heterozygous variants consistent with dominant disease with incomplete penetrance were ascertained, and variants with predicted functional consequence were prioritized for analysis. Pedigree-specific p-values were calculated as the probability of all affected members in the pedigree being carriers, given that at least one is a carrier. RESULTS Preliminary results identified 3727 heterozygous rare variants; 1282 were predicted to be functionally consequential. Twenty-three genes had variants of interest in ≥3 families, where some genes had different variants in each family, giving a total of 50 variants. Variant validation via Sanger sequencing of the families and unrelated unaffected controls excluded variants that were sequencing errors or common variants not in databases, leaving four genes with candidate variants in ≥3 families. Of these, candidate variants in two genes consistently segregate with NSCLP as a dominant variant with incomplete penetrance: ACSS2 and PHYH. CONCLUSION Rare variants found at the same gene in all affected individuals in several families are likely directly related to NSCLP.

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Section: Discussionmentioning

confidence: 97%

Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate

Aylward

Cai

Lee

et al. 2016

Genetic Epidemiology

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“…Besides proteinprotein interactions from 12 different resources (including HPRD, BioGrid, IntAct, DIP, BIND and Reactome databases) as well as four interaction maps produced by computational predictions and two high‐throughput yeast‐2‐hybrid screens, UniHI 7 also comprises curated transcriptional regulatory interactions from three complementary databases TRANSFAC, miRTarBase and HTRIdb. In addition to these interactions, the service also integrated drug target information from DrugBank that can be mapped and visualized online without having to download, manually process and load the data into an external standalone application 68. The data can be filtered by the users (e.g., number of PubMed references, small‐scale or large‐scale experiments, direct or indirect connection, binary or complex interaction).…”

Section: Ppi Studies Combining In Vitro and In Silico Approaches: Fmentioning

confidence: 99%

Drug‐Like ProteinProtein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

Villoutreix

Kuenemann

Poyet

et al. 2014

Molecular Informatics

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Fundamental processes in living cells are largely controlled by macromolecular interactions and among them, protein–protein interactions (PPIs) have a critical role while their dysregulations can contribute to the pathogenesis of numerous diseases. Although PPIs were considered as attractive pharmaceutical targets already some years ago, they have been thus far largely unexploited for therapeutic interventions with low molecular weight compounds. Several limiting factors, from technological hurdles to conceptual barriers, are known, which, taken together, explain why research in this area has been relatively slow. However, this last decade, the scientific community has challenged the dogma and became more enthusiastic about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages. In this review article, written for the 2014 International Summer School in Chemoinformatics (Strasbourg, France), we discuss in silico tools (essentially post 2012) and databases that can assist the design of low molecular weight PPI modulators (these tools can be found at www.vls3d.com). We first introduce the field of protein–protein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs. Then, we illustrate how in silico methods can be used and combined with experimental work to identify PPI modulators.

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“…The Hibernate library was employed to handle communications between StemCellNet and the database. Gene annotation was imported from UniHI database (21). Gene and protein identifiers used in the mapping function were uploaded from HGNC and bioDBnet resources (24,34).…”

Section: Methodsmentioning

confidence: 99%

“…To provide a more comprehensive coverage, we therefore also included molecular interactions for both human and mouse, identified in other types of cells. These additional molecular interactions (∼300 000) were imported from different resources (21,22). This expanded dataset enables the user to query interaction data for 36 023 distinct genes or proteins.…”

Section: Data Integrated In Stemcellnetmentioning

confidence: 99%

StemCellNet: an interactive platform for network-oriented investigations in stem cell biology

Pinto

Kalathur

Machado

et al. 2014

Nucleic Acids Research

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Stem cells are characterized by their potential for self-renewal and their capacity to differentiate into mature cells. These two key features emerge through the interplay of various factors within complex molecular networks. To provide researchers with a dedicated tool to investigate these networks, we have developed StemCellNet, a versatile web server for interactive network analysis and visualization. It rapidly generates focused networks based on a large collection of physical and regulatory interactions identified in human and murine stem cells. The StemCellNet web-interface has various easy-to-use tools for selection and prioritization of network components, as well as for integration of expression data provided by the user. As a unique feature, the networks generated can be screened against a compendium of stemness-associated genes. StemCellNet can also indicate novel candidate genes by evaluating their connectivity patterns. Finally, an optional dataset of generic interactions, which provides large coverage of the human and mouse proteome, extends the versatility of StemCellNet to other biomedical research areas in which stem cells play important roles, such as in degenerative diseases or cancer. The StemCellNet web server is freely accessible at http://stemcellnet.sysbiolab.eu.

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UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks

Cited by 83 publications

References 49 publications

Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate

Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate

Drug‐Like ProteinProtein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

StemCellNet: an interactive platform for network-oriented investigations in stem cell biology

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