Database of RNA binding protein expression and disease dynamics (READ DB)

Hashemikhabir, Seyedsasan; Neelamraju, Yaseswini; Janga, Sarath Chandra

doi:10.1093/database/bav072

Cited by 9 publications

(9 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A second example involves the construction of RNA Binding Protein (RBP) Expression and Disease Dynamics database (READ DB), a non-redundant, curated database of human RBPs. Adding to other RBP annotations such as RNA and protein expression levels, RNA recognition motifs and predicted binding targets, they included scored diseases associations from MalaCards, providing the disease dynamics aspects of RBPs in the context of post-transcriptional regulatory networks (39). …”

Section: Use Casesmentioning

confidence: 99%

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

et al. 2016

View full text Add to dashboard Cite

The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symptoms, Anatomical Context, Drugs, Genetic Tests, Variations and Publications. The Aliases and Classifications section reflects an algorithm for disease name integration across often-conflicting sources, providing effective annotation consolidation. A central feature is a balanced Genes section, with scores reflecting the strength of disease-gene associations. This is accompanied by other gene-related disease information such as pathways, mouse phenotypes and GO-terms, stemming from MalaCards’ affiliation with the GeneCards Suite of databases. MalaCards’ capacity to inter-link information from complementary sources, along with its elaborate search function, relational database infrastructure and convenient data dumps, allows it to tackle its rich disease annotation landscape, and facilitates systems analyses and genome sequence interpretation. MalaCards adopts a ‘flat’ disease-card approach, but each card is mapped to popular hierarchical ontologies (e.g. International Classification of Diseases, Human Phenotype Ontology and Unified Medical Language System) and also contains information about multi-level relations among diseases, thereby providing an optimal tool for disease representation and scrutiny.

show abstract

Section: Use Casesmentioning

confidence: 99%

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Application of commercial pathway analysis software or public tools such as DAVID (Database for Annotation, Visualization and Integrated Discovery) (Huang et al, 2009) can identify functionally clustered candidates among DEGs. Thereafter, functional gene ontology enrichment can be enhanced by expanding the relationships of DEGs by overlaying publically available protein-protein (Rolland et al, 2014) and protein-DNA (Hume et al, 2015), protein-RNA interaction data (Hashemikhabir et al, 2015), along with iSyTE lens expression and evidence-based data. This approach recently applied to microarray-identified DEGs in Mafg−/−:MafKk+/− mouse lenses led to the derivation of a small Maf regulatory sub-network that primarily regulates non-crystallin genes linked to cataract (Agrawal et al, 2015; Anand et al, 2015).…”

Section: Future Of Lens Research: Toward Lens Systems Biologymentioning

confidence: 99%

Systems biology of lens development: A paradigm for disease gene discovery in the eye

Anand

Lachke

2017

Experimental Eye Research

View full text Add to dashboard Cite

Over the past several decades, the biology of the developing lens has been investigated using molecular genetics-based approaches in various vertebrate model systems. These efforts, involving target gene knockouts or knockdowns, have led to major advances in our understanding of lens morphogenesis and the pathological basis of cataracts, as well as of other lens related eye defects. In particular, we now have a functional understanding of regulators such as Pax6, Six3, Sox2, Oct1 (Pou2f1), Meis1, Pnox1, Zeb2 (Sip1), Mab21l1, Foxe3, Tfap2a (Ap2-alpha), Pitx3, Sox11, Prox1, Sox1, c-Maf, Mafg, Mafk, Hsf4, Fgfrs, Bmp7, and Tdrd7 in this tissue. However, whether these individual regulators interact or their targets overlap, and the significance of such interactions during lens morphogenesis, is not well defined. The arrival of high-throughput approaches for gene expression profiling (microarrays, RNA-sequencing (RNA-seq), etc.), which can be coupled with chromatin immunoprecipitation (ChIP) or RNA immunoprecipitation (RIP) assays, along with improved computational resources and publically available datasets (e.g. those containing comprehensive protein-protein, protein-DNA information), presents new opportunities to advance our understanding of the lens tissue on a global systems level. Such systems-level knowledge will lead to the derivation of the underlying lens gene regulatory network (GRN), defined as a circuit map of the regulator-target interactions functional in lens development, which can be applied to expedite cataract gene discovery. In this review, we cover the various systems-level approaches such as microarrays, RNA-seq, and ChIP that are already being applied to lens studies and discuss strategies for assembling and interpreting these vast amounts of high-throughput information for effective dispersion to the scientific community. In particular, we discuss strategies for effective interpretation of this new information in the context of the rich knowledge obtained through the application of traditional single-gene focused experiments on the lens. Finally, we discuss our vision for integrating these diverse high-throughput datasets in a single web-based user-friendly tool iSyTE (integrated Systems Tool for Eye gene discovery) – a resource that is already proving effective in the identification and characterization of genes linked to lens development and cataract. We anticipate that application of a similar approach to other ocular tissues such as the retina and the cornea, and even other organ systems, will significantly impact disease gene discovery.

show abstract

“…Therefore, it is likely that the identified human RBPs that interact with viral proteins assist in the viral pathogenesis. Furthermore, we also observed that ~65% of annotated human RBPs [55] were in immediate neighborhood (obtained from BioGRID [56], shown at the center in Fig. 1A) of virus-protein interacting RBPs and could indirectly regulate the SARS-CoV-2 proteins.…”

Section: Protein-protein Interaction Network Analysis For Sars-cov-2 mentioning

confidence: 70%

“…To date, the PWMs are available only for a small fraction of the experimentally known human RBPs [83]. Thus, our analysis represents an understanding of post-transcriptional interactions for ~7.5% of total RBPs collected from multiple studies [24,55,84]. Importantly, the binding pattern of the RBP motifs across the entire normalized length of the virus suggests that, several of human RBPs could be titrated across the viral genome (Fig.…”

Section: Motif Enrichment Analysis Reveals Potential Human Rbps Titramentioning

confidence: 99%

Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans

Srivastava

Daulatabad

Srivastava

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

AbstractThe outbreak of a novel coronavirus SARS-CoV2 responsible for COVID-19 pandemic has caused worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2 mediated alteration on post-transcriptional gene regulation across human tissues remains elusive. In this study, we systematically dissected the crosstalk and dysregulation of human post-transcriptional regulatory networks governed by RNA binding proteins (RBPs) and micro-RNAs (miRs), due to SARS-CoV-2 infection. We uncovered that 13 out of 29 SARS-CoV-2 encoded proteins directly interact with 51 human RBPs of which majority of them were abundantly expressed in gonadal tissues and immune cells. We further performed functional analysis of differentially expressed genes in mock treated versus SARS-CoV-2 infected lung cells that revealed an enrichment for immune response, cytokine mediated signaling, and metabolism associated genes. This study also characterized the alternative splicing events in SARS-CoV-2 infected cells compared to control demonstrating that skipped exons and mutually exclusive exons were the most abundant events that potentially contributed to differential outcomes in response to viral infection. Motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed an enrichment for RBPs such as SRSFs, PCBPs, ELAVs and HNRNPs illustrating the sponging of RBPs by SARS-CoV-2 genome. Similar analysis to study the interactions of miRs with SARS-CoV-2 revealed the potential for several miRs to be sponged, suggesting that these interactions may contribute to altered pos-transcriptional regulation across human tissues. Given the need to understand the interactions of SARS-CoV-2 with key pos-transcriptional regulators in the human genome, this study provides a systematic analysis to dissect the role of dysregulated post-transcriptional regulatory networks controlled by RBPs and miRs, across tissues types during SARS-CoV2 infection.

show abstract

Database of RNA binding protein expression and disease dynamics (READ DB)

Cited by 9 publications

References 26 publications

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

Systems biology of lens development: A paradigm for disease gene discovery in the eye

Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans

Contact Info

Product

Resources

About