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AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, Mario Albrecht
2010 Nucleic Acids Research  
Here, we present our new software workflow composed of the open-source application AltAnalyze and the Cytoscape plugin DomainGraph.  ...  Both programs provide an intuitive and comprehensive end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains  ...  Cline and Gary Howard for their valuable advice on the development of AltAnalyze and DomainGraph, and on the article.  ... 
doi:10.1093/nar/gkq405 pmid:20513647 pmcid:PMC2896198 fatcat:ehwgu6jxpfgvnouesxqgkmottu

Stem cell pluripotency: Alternative modes of transcription regulation

Nathan Salomonis, Bruce R. Conklin
2010 Cell Cycle  
These predictions can be further visualized in programs such as DomainGraph 10 as a means to see which transcripts are specifically affected by alternative exon expression and how these changes affect  ...  Illustration depicting the analysis of whole-genome transcript expression data, in the context of alternative mrNA transcripts and functional outcomes with the application AltAnalyze.  ... 
doi:10.4161/cc.9.16.12888 pmid:20814242 pmcid:PMC3866144 fatcat:ptgzsvtfgbevve35ltiorlcipe

Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events

Pascal Gellert, Mizue Teranishi, Katharina Jenniches, Piera De Gaspari, David John, Karsten grosse Kreymborg, Thomas Braun, Shizuka Uchida
2011 Nucleic Acids Research  
Here, we show that the newly developed Gene Array Analyzer (GAA), which evolved from our previously published Exon Array Analyzer (EAA), enables economic and user-friendly analysis of alternative splicing  ...  Exon arrays are regularly used to analyze differential splicing events.  ...  ACCESSION NUMBERS Gene Expression Omnibus: GSE30429 and GSE33183.  ... 
doi:10.1093/nar/gkr1110 pmid:22123740 pmcid:PMC3315316 fatcat:bqkuamjg5vfsfnzbnsfr6s3xcu

Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

Ting-Yu Chang, Yu-Hsuan Wu, Cheng-Chung Cheng, Hsei-Wei Wang
2011 Nucleic Acids Research  
We analyzed KSHV-controlled AS using high-density microarrays capable of detecting all exons in the human genome.  ...  Splicing variants and altered exon-intron usage in infected LEC were found, and these correlated with protein domain modification.  ...  Science Council (NSC), of the National Yang-Ming University VGH Genome Research Center and the shRNA knockdown plasmids provided by National RNAi Core Facility, Taiwan.  ... 
doi:10.1093/nar/gkr405 pmid:21646333 pmcid:PMC3167639 fatcat:klocnbchaffkfg7rwllab7m6pm

Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer

Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Al Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri, Osman El-Maarri
2014 PLoS ONE  
In this study, we analyze these driver genes at three levels using exon array data -gene, exon and network. Gene level analysis revealed a small subset to experience differential expression.  ...  These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA).  ...  Balwi and Hussein in providing facilities for conducting experiments and analyses is acknowledged. Author Contributions  ... 
doi:10.1371/journal.pone.0110134 pmid:25335079 pmcid:PMC4204855 fatcat:zdnqmcqt3jhn5b7sripjgorvp4

Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells

S Scott Whitmore, Terry A Braun, Jessica M Skeie, Christine M Haas, Elliott H Sohn, Edwin M Stone, Todd E Scheetz, Robert F Mullins
2013 Molecular Vision  
The complement factor H (CFH) genotype was also assessed, and differential expression was analyzed regarding high AMD risk (YH/HH) and low AMD risk (YY) genotypes.  ...  Differentially expressed genes were annotated using the Database for Annotation, Visualization and Integrated Discovery (DAVID), and gene set enrichment analysis (GSEA) was performed on RPE-specific and  ...  No transcripts flagged by AltAnalyze as putative splicing events appeared to be alternatively spliced upon close visual inspection of the probeset data in DomainGraph.  ... 
pmid:24265543 pmcid:PMC3834599 fatcat:dnnnw3ylc5bcdnaidnlez4tlgi

DIGGER: exploring the functional role of alternative splicing in protein interactions

Zakaria Louadi, Kevin Yuan, Alexander Gress, Olga Tsoy, Olga V Kalinina, Jan Baumbach, Tim Kacprowski, Markus List
2020 Nucleic Acids Research  
We overcome this barrier by integrating protein-protein interactions, domain-domain interactions and residue-level interactions information to lift exon expression analysis to a network level.  ...  Our user-friendly database DIGGER is available at and allows users to seamlessly switch between isoform and exon-centric views of the interactome and to extract sub-networks  ...  Nucleic Acids Research, 2021, Vol. 49, Database issue D317 method (18) and DomainGraph (22) that only focus on the isoform interactions or PPIXpress that analyzes transcript expression data (24) .  ... 
doi:10.1093/nar/gkaa768 pmid:32976589 fatcat:3m2sw6qcd5e4zh7djobfzezp34

BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments

Arianna Consiglio, Massimo Carella, Giorgio De Caro, Gianfranco Delle Foglie, Candida Giovannelli, Giorgio Grillo, Massimo Ianigro, Flavio Licciulli, Orazio Palumbo, Ada Piepoli, Elena Ranieri, Sabino Liuni
2012 BMC Bioinformatics  
In this paper we describe BEAT, an integrated userfriendly bioinformatics framework to store, analyze and visualize exon arrays datasets.  ...  The exon array technology, with more than five million data points, can detect approximately one million exons, and it allows performing analyses at both gene and exon level.  ...  We would like to thank Ernesto Picardi for his helpful comments and discussions about exon array statistical analysis, Nicola Losito for helping us with servers and data base management, Raffaella Stallone  ... 
doi:10.1186/1471-2105-13-s4-s21 pmid:22536968 pmcid:PMC3314565 fatcat:vxfvkhavozh5bfcoemasocgdha

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity

Bishakha Roy, Larisa M. Haupt, Lyn R. Griffiths
2013 Current Genomics  
Bioinformatics provides an important approach to study mRNA and protein diversity by various tools such as expressed sequence tag (EST) sequences obtained from completely processed mRNA.  ...  Numerous databases and online bioinformatic tools are available for the detection and analysis of AS.  ...  AltAnalyze and the Cytoscape plugin DomainGraph programs offer an intuitive and comprehensive solution for the analysis and visualization of AS data from Affymetrix exon and gene arrays at the level of  ... 
doi:10.2174/1389202911314030004 pmid:24179441 pmcid:PMC3664468 fatcat:h7pkjfvxezauznlx3dthpyf2ce

Novel analysis approaches to context-dependent molecular networks [article]

Dorothea Emig, Universität Des Saarlandes, Universität Des Saarlandes
We further use gene expression data to identify tissue-specific protein interactions and their functional implications.  ...  We describe our software DomainGraph that allows for visually exploring protein variants and their interactions in different biological conditions.  ...  A visual investigation highlights that exons 11 and 12 are Figure 6 . 2 : 62 DomainGraph table view for AltAnalyze alternative exon statistics.  ... 
doi:10.22028/d291-26027 fatcat:ilbifw5rzbad3khxpibjn3qhcu

CtIP-mediated alternative mRNA splicing finetunes the DNA damage response [article]

Rosario Prados-Carvajal, Guillermo Rodríguez-Real, Gabriel Gutierrez-Pozo, Pablo Huertas
2019 bioRxiv   pre-print
On the contrary, expression of the full length PIF1 facilitates those early events, but increases the sensitivity to DNA damaging agents if the expression is maintained long-term.  ...  Interestingly, timely expression of vPIF1 is required for optimal survival to exposure to DNA damaging agents, but early expression of this isoform delays early events of the DNA damage response.  ...  AltAnalyze and DomainGraph: Analyzing and visualizing exon expression data. Nucleic Acids Res. 38, 755-762. Fan, J., Yang, X., Wang, W., Wood, W.H., Becker, K.G., and Gorospe, M. (2002).  ... 
doi:10.1101/849547 fatcat:dou37hxq3zgu3cjf4dlxh5mogu

An adipocyte light-Opsin 3 pathway regulates the circadian clock and energy balance [article]

Shruti Vemaraju, Gowri Nayak, Ethan D Buhr, Yoshinobu Odaka, Kevin X Zhang, Julie A Mocko, April N Smith, Brian A Upton, Jesse J Zhan, Vishnupriya J Borra, Elise Bernhard, Kazutoshi Murakami (+12 others)
2018 bioRxiv   pre-print
Examples include the visual system, where photoreceptor signals are processed into virtual images, and the circadian system, where light entrains a physiological clock.  ...  These data indicate an important role for peripheral light sensing in mammals and may have broad implications for human health given the unnatural lighting conditions in which we live.  ...  AltAnalyze and DomainGraph: Analyzing and visualizing exon expression 379 data. Nucleic Acids Res. 38, (2010). 17 . 17 Khan, T. et al.  ... 
doi:10.1101/368373 fatcat:blk7bqahynbghlve5jpquzhvy4

Adaptive thermogenesis in mice requires adipocyte light-sensing via Opsin 3 [article]

Gowri Nayak, Shruti Vemaraju, Kevin X Zhang, Yoshinobu Odaka, Ethan D Buhr, Amanda Holt-Jones, April N Smith, Brian A Upton, Jesse J Zhan, Nicolas Diaz, Kazutoshi Murakami, Shane D'Souza (+14 others)
2019 bioRxiv   pre-print
Examples include the visual system, where photoreceptor signals are interpreted as images, and the circadian system, where light entrains a physiological clock.  ...  These data suggest the hypothesis that in mice, a local, OPN3-dependent light response in adipocytes is a mechanism for regulation of energy homeostasis.  ...  Daily, MD Research Fund to University of Washington, and unrestricted grants to the University of Washington and from Research to Prevent Blindness.  ... 
doi:10.1101/721381 fatcat:5epcboefgbhqrlaxo6usgwfshy

From condition-specific interactions towards the differential complexome of proteins [article]

Thorsten Will, Universität Des Saarlandes
PPIXpress allows to exploit the abundance of existing expression data to generate specific interactomes, which can even consider alternative splicing events when protein isoforms can be related to the  ...  In this thesis, we present and demonstrate four software tools that unlock the cellular wiring in a condition-specific manner and promise a deeper understanding of what happens upon cell fate transitions  ...  When linked to the AS analysis tool AltAnalyze, DomainGraph can highlight protein domains in DDINs that are affected by differential exon usage [181] .  ... 
doi:10.22028/d291-32493 fatcat:f2kkrll3sfepnh2x445ixsox3a