DOCSLIB.ORG

Mitoxplorer, a Visual Data Mining Platform To

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, Cecilia Garcia-Perez, José Villaveces, Salma Gamal, Giovanni Cardone, Fabiana Perocchi, et al. To cite this version: Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, et al.. mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dy- namics and mutations. Nucleic Acids Research, Oxford University Press, 2020, 10.1093/nar/gkz1128. hal-02394433 HAL Id: hal-02394433 https://hal-amu.archives-ouvertes.fr/hal-02394433 Submitted on 4 Dec 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gkz1128 Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz1128/5651332 by Bibliothèque de l'université la Méditerranée user on 04 December 2019 mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim1,†, Prasanna Koti1,†, Adrien Bonnard2, Fabio Marchiano3, Milena Durrbaum¨ 1, Cecilia Garcia-Perez4, Jose Villaveces1, Salma Gamal1, Giovanni Cardone1, Fabiana Perocchi4, Zuzana Storchova1,5 and Bianca H. Habermann 1,3,* 1Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, 2Aix-Marseille University, INSERM, TAGC U1090, 13009 Marseille, France, 3Aix-Marseille University, CNRS, IBDM UMR 7288, 13009 Marseille, France, 4Functional Genomics of Mitochondrial Signaling, Gene Center, Ludwig Maximilian University (LMU), Munich, Germany and 5Department of Molecular Genetics, TU Kaiserslautern, Paul Ehrlich Strasse 24, 67663 Kaiserslautern, Germany Received May 30, 2019; Revised October 30, 2019; Editorial Decision November 13, 2019; Accepted November 18, 2019 ABSTRACT aiding experimental scientists to quantify mitochon- drial expression dynamics. Mitochondria participate in metabolism and signal- ing. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochon- INTRODUCTION drial function (mito-genes) in various cell types, con- Enormous amounts of transcriptomic data are publicly ditions and organisms. Yet, we lack an easy way of available for exploration. This richness of data gives us the extracting these data for mito-genes. Here, we intro- unique opportunity to explore the behavior of individual duce the visual data mining platform mitoXplorer, genes or groups of genes within a vast variety of different which integrates expression and mutation data of cell types, developmental or disease conditions or in differ- mito-genes with a manually curated mitochondrial ent species. By integrating these data in a sophisticated way, interactome containing ∼1200 genes grouped in 38 we may be capable to discover new dependencies between mitochondrial processes. User-friendly analysis and genesorprocesses. Specific databases are available for mining and exploring visualization tools allow to mine mitochondrial ex- disease-associated data, such as The Cancer Genome Atlas pression dynamics and mutations across various (TCGA, https://portal.gdc.cancer.gov/)(1), or the Interna- datasets from four model species including human. tional Cancer Consortium Data Portal (ICGC, https://dcc. To test the predictive power of mitoXplorer, we quan- icgc.org/)(2). Especially cancer data portals allow users to tify mito-gene expression dynamics in trisomy 21 perform deeper exploration of expression changes of indi- cells, as mitochondrial defects are frequent in tri- vidual genes or gene groups in different tumor types ((1– somy 21. We uncover remarkable differences in the 3); for a review on available cancer data portals, see (4)). regulation of the mitochondrial transcriptome and Expression Atlas (https://www.ebi.ac.uk/gxa/home)onthe proteome in one of the trisomy 21 cell lines, caused other hand provides pre-processed data from a large variety by dysregulation of the mitochondrial ribosome and of different studies in numerous species (5). Indeed, the ma- resulting in severe defects in oxidative phosphory- jority of transcriptomic datasets are not related to cancer and are stored in public repositories such as Gene Expres- lation. With the newly developed Fiji plugin mito- sion Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) Morph, we identify mild changes in mitochondrial (6), DDBJ Omics Archive (https://www.ddbj.nig.ac.jp/gea/ morphology in trisomy 21. Taken together, mitoX- index-e.html)(7), or ArrayExpress (https://www.ebi.ac.uk/ plorer (http://mitoxplorer.ibdm.univ-mrs.fr)isauser- arrayexpress/)(8). Currently, it is not straightforward to in- friendly, web-based and freely accessible software, tegrate data from these repositories without at least basic programming knowledge. *To whom correspondence should be addressed. Tel: +33 4 91 26 92 36; Email: [email protected] †The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors. C The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Nucleic Acids Research, 2019 Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz1128/5651332 by Bibliothèque de l'université la Méditerranée user on 04 December 2019 Next to extracting reliable information from -omics tional assignments of mito-proteins. Moreover, proteomic datasets, it is equally important to support interactive data studies describing the mitochondrial proteome can suffer visualization. This is a key element for a user-guided ex- from a high false-positive rate (23), whereas computational ploration and interpretation of complex data, facilitating prediction or machine learning in most cases lack experi- the generation of biologically relevant hypotheses––a pro- mental confirmation (37). As a consequence, none of the cess referred to as visual data mining (VDM, reviewed e.g. published mitochondrial interactomes available to date can in (9)). Therefore, essentially all online data portals provide be taken without further manual curation. Moreover, these graphical tools for data exploration. lists are not integrated with any available data analysis tool What is fundamentally lacking is a user-centric, web- to explore mitochondrial expression dynamics under vary- based and interactive platform for data integration of a set ing conditions or in different tissues or species. of selected genes or proteins sharing the same cellular func- In this study, we present mitoXplorer, a web-based, tion(s). The benefits of such a tool are evident: first, it would highly interactive visual data mining (VDM) platform de- give us the possibility to explore the expression dynamics signed to specifically mine the dynamics of a manually cu- and the presence of mutations in this set of selected genes rated gene set with mitochondrial functions in transcrip- across many different conditions, tissues and species. Sec- tome, proteome, as well as mutation-based data. To achieve ond, by integrating data using enrichment techniques, for this, mitoXplorer integrates -omics data with our hand- instance with epigenetic data or by network analysis using curated mitochondrial interactomes for currently four dif- the cellular interactome(s), it would allow us to identify the ferent model species. With mitoXplorer, we can explore the mechanisms that regulate the expression dynamics of the expression dynamics, as well as mutations of mito-genes and selected gene set. their associated mitochondrial processes (mito-processes) One interesting set of genes are mitochondria-associated across a large variety of different -omics datasets without genes (mito-genes): in other words all genes, whose encoded the need of programming knowledge. MitoXplorer pro- proteins localize to mitochondria and fulfill their cellular vides users with dynamic and interactive figures, which in- function within this organelle. Mito-genes are well-suited stantly display information on mitochondrial gene func- for such a systematic analysis, because we have a relatively tions and protein-protein interactions. Users can analyze complete knowledge of their identity and can categorize publicly available data stored in our mitoXlorer database them according to their mitochondrial functions (10). This or upload their own data for integration with our hand- aprioriknowledge can help us in mining and exploring the curated mitochondrial interactome. In order to demon- expression dynamics of mito-genes
Recommended publications
  • ACTR2 Antibody / Arp2 (RQ5865)

    ACTR2 Antibody / Arp2 (RQ5865)

    ACTR2 Antibody / Arp2 (RQ5865) Catalog No. Formulation Size RQ5865 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human, Mouse, Rat, Monkey Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Affinity purified Buffer Lyophilized from 1X PBS with 2% Trehalose and 0.025% sodium azide UniProt P61160 Applications Western blot : 0.5-1ug/ml Immunohistochemistry : 1-2ug/ml Immunofluorescence : 2-4ug/ml Flow cytometry : 1-3ug/million cells Direct ELISA : 0.1-0.5ug/ml Limitations This ACTR2 antibody is available for research use only. IHC staining of FFPE human breast cancer with ACTR2 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. Immunofluorescent staining of FFPE human A549 cells with ACTR2 antibody (green) and DAPI nuclear stain (blue). HIER: steam section in pH6 citrate buffer for 20 min. Western blot testing of 1) rat kidney, 2) rat spleen, 3) mouse HEPA1-6, 4) mouse SP2/0, 5) monkey COS-7 and human 6) U-87 MG, 7) Jurkat, 8) PC-3 and 9) U-2 OS lysate with ACTR2 antibody. Predicted molecular weight ~45 kDa. Flow cytometry testing of human A431 cells with ACTR2 antibody at 1ug/million cells (blocked with goat sera); Red=cells alone, Green=isotype control, Blue= ACTR2 antibody. Flow cytometry testing of mouse ANA-1 cells with ACTR2 antibody at 1ug/million cells (blocked with goat sera); Red=cells alone, Green=isotype control, Blue= ACTR2 antibody. Description The specific function of this gene has not yet been determined; however, the protein it encodes is known to be a major constituent of the ARP2/3 complex.
  • Biomarker Discovery for Chronic Liver Diseases by Multi-Omics

    Biomarker Discovery for Chronic Liver Diseases by Multi-Omics

    www.nature.com/scientificreports OPEN Biomarker discovery for chronic liver diseases by multi-omics – a preclinical case study Daniel Veyel1, Kathrin Wenger1, Andre Broermann2, Tom Bretschneider1, Andreas H. Luippold1, Bartlomiej Krawczyk1, Wolfgang Rist 1* & Eric Simon3* Nonalcoholic steatohepatitis (NASH) is a major cause of liver fbrosis with increasing prevalence worldwide. Currently there are no approved drugs available. The development of new therapies is difcult as diagnosis and staging requires biopsies. Consequently, predictive plasma biomarkers would be useful for drug development. Here we present a multi-omics approach to characterize the molecular pathophysiology and to identify new plasma biomarkers in a choline-defcient L-amino acid-defned diet rat NASH model. We analyzed liver samples by RNA-Seq and proteomics, revealing disease relevant signatures and a high correlation between mRNA and protein changes. Comparison to human data showed an overlap of infammatory, metabolic, and developmental pathways. Using proteomics analysis of plasma we identifed mainly secreted proteins that correlate with liver RNA and protein levels. We developed a multi-dimensional attribute ranking approach integrating multi-omics data with liver histology and prior knowledge uncovering known human markers, but also novel candidates. Using regression analysis, we show that the top-ranked markers were highly predictive for fbrosis in our model and hence can serve as preclinical plasma biomarkers. Our approach presented here illustrates the power of multi-omics analyses combined with plasma proteomics and is readily applicable to human biomarker discovery. Nonalcoholic fatty liver disease (NAFLD) is the major liver disease in western countries and is ofen associated with obesity, metabolic syndrome, or type 2 diabetes.
  • Seq2pathway Vignette

    Seq2pathway Vignette

    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
  • Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome

    Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome

    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome Edward L. Huttlin1*, Raphael J. Bruckner1,3, Jose Navarrete-Perea1, Joe R. Cannon1,4, Kurt Baltier1,5, Fana Gebreab1, Melanie P. Gygi1, Alexandra Thornock1, Gabriela Zarraga1,6, Stanley Tam1,7, John Szpyt1, Alexandra Panov1, Hannah Parzen1,8, Sipei Fu1, Arvene Golbazi1, Eila Maenpaa1, Keegan Stricker1, Sanjukta Guha Thakurta1, Ramin Rad1, Joshua Pan2, David P. Nusinow1, Joao A. Paulo1, Devin K. Schweppe1, Laura Pontano Vaites1, J. Wade Harper1*, Steven P. Gygi1*# 1Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA. 2Broad Institute, Cambridge, MA, 02142, USA. 3Present address: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA. 4Present address: Merck, West Point, PA, 19486, USA. 5Present address: IQ Proteomics, Cambridge, MA, 02139, USA. 6Present address: Vor Biopharma, Cambridge, MA, 02142, USA. 7Present address: Rubius Therapeutics, Cambridge, MA, 02139, USA. 8Present address: RPS North America, South Kingstown, RI, 02879, USA. *Correspondence: [email protected] (E.L.H.), [email protected] (J.W.H.), [email protected] (S.P.G.) #Lead Contact: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
  • Selective Induction of Apoptosis in HIV-Infected Macrophages

    Selective Induction of Apoptosis in HIV-Infected Macrophages

    Selective Induction of Apoptosis in HIV-infected Macrophages by Simon Xin Min Dong A thesis submitted in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Microbiology and Immunology Department of Biochemistry, Microbiology, and Immunology Faculty of Medicine University of Ottawa © Simon Xin Min Dong, Ottawa, Canada, 2020 Abstract The eradication of Human Immunodeficiency Virus (HIV) from infected patients is one of the major medical problems of our time, primarily due to HIV reservoir formation. Macrophages play important roles in HIV reservoir formation: once infected, they shield HIV against host anti-viral immune responses and anti-retroviral therapies, help viral spread and establish infection in anatomically protected sites. Thus, it is imperative to selectively induce the apoptosis of HIV-infected macrophages for a complete cure of this disease. I hypothesize that HIV infection dysregulates the expression of some specific genes, which is essential to the survival of infected host cells, and these genes can be targeted to selectively induce the apoptosis of HIV-infected macrophages. My objective is to identify the genes that can be targeted to eradicate HIV reservoir in macrophages, and to briefly elucidate the mechanism of cell death induced by targeting one of the identified genes. A four-step strategy was proposed to reach the goal. First, 90k shRNA lentivirus pool technology and microarray analysis were employed in a genome-wide screen of genes and 28 promising genes were found. Second, siRNA silencing was applied to validate these genes with 2 different HIV-1 viruses; as a result, 4 genes, Cox7a2, Znf484, Cdk2, and Cstf2t, were identified to be novel gene targets.
  • Location Analysis of Estrogen Receptor Target Promoters Reveals That

    Location Analysis of Estrogen Receptor Target Promoters Reveals That

    Location analysis of estrogen receptor ␣ target promoters reveals that FOXA1 defines a domain of the estrogen response Jose´ e Laganie` re*†, Genevie` ve Deblois*, Ce´ line Lefebvre*, Alain R. Bataille‡, Franc¸ois Robert‡, and Vincent Gigue` re*†§ *Molecular Oncology Group, Departments of Medicine and Oncology, McGill University Health Centre, Montreal, QC, Canada H3A 1A1; †Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 1Y6; and ‡Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montre´al, Montreal, QC, Canada H2W 1R7 Communicated by Ronald M. Evans, The Salk Institute for Biological Studies, La Jolla, CA, July 1, 2005 (received for review June 3, 2005) Nuclear receptors can activate diverse biological pathways within general absence of large scale functional data linking these putative a target cell in response to their cognate ligands, but how this binding sites with gene expression in specific cell types. compartmentalization is achieved at the level of gene regulation is Recently, chromatin immunoprecipitation (ChIP) has been used poorly understood. We used a genome-wide analysis of promoter in combination with promoter or genomic DNA microarrays to occupancy by the estrogen receptor ␣ (ER␣) in MCF-7 cells to identify loci recognized by transcription factors in a genome-wide investigate the molecular mechanisms underlying the action of manner in mammalian cells (20–24). This technology, termed 17␤-estradiol (E2) in controlling the growth of breast cancer cells. ChIP-on-chip or location analysis, can therefore be used to deter- We identified 153 promoters bound by ER␣ in the presence of E2. mine the global gene expression program that characterize the Motif-finding algorithms demonstrated that the estrogen re- action of a nuclear receptor in response to its natural ligand.
  • Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function

    Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function

    Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human.
  • Multi-Targeted Mechanisms Underlying the Endothelial Protective Effects of the Diabetic-Safe Sweetener Erythritol

    Multi-Targeted Mechanisms Underlying the Endothelial Protective Effects of the Diabetic-Safe Sweetener Erythritol

    Multi-Targeted Mechanisms Underlying the Endothelial Protective Effects of the Diabetic-Safe Sweetener Erythritol Danie¨lle M. P. H. J. Boesten1*., Alvin Berger2.¤, Peter de Cock3, Hua Dong4, Bruce D. Hammock4, Gertjan J. M. den Hartog1, Aalt Bast1 1 Department of Toxicology, Maastricht University, Maastricht, The Netherlands, 2 Global Food Research, Cargill, Wayzata, Minnesota, United States of America, 3 Cargill RandD Center Europe, Vilvoorde, Belgium, 4 Department of Entomology and UCD Comprehensive Cancer Center, University of California Davis, Davis, California, United States of America Abstract Diabetes is characterized by hyperglycemia and development of vascular pathology. Endothelial cell dysfunction is a starting point for pathogenesis of vascular complications in diabetes. We previously showed the polyol erythritol to be a hydroxyl radical scavenger preventing endothelial cell dysfunction onset in diabetic rats. To unravel mechanisms, other than scavenging of radicals, by which erythritol mediates this protective effect, we evaluated effects of erythritol in endothelial cells exposed to normal (7 mM) and high glucose (30 mM) or diabetic stressors (e.g. SIN-1) using targeted and transcriptomic approaches. This study demonstrates that erythritol (i.e. under non-diabetic conditions) has minimal effects on endothelial cells. However, under hyperglycemic conditions erythritol protected endothelial cells against cell death induced by diabetic stressors (i.e. high glucose and peroxynitrite). Also a number of harmful effects caused by high glucose, e.g. increased nitric oxide release, are reversed. Additionally, total transcriptome analysis indicated that biological processes which are differentially regulated due to high glucose are corrected by erythritol. We conclude that erythritol protects endothelial cells during high glucose conditions via effects on multiple targets.
  • CRAVAT 4: Cancer-Related Analysis of Variants Toolkit David L

    CRAVAT 4: Cancer-Related Analysis of Variants Toolkit David L

    Cancer Focus on Computer Resources Research CRAVAT 4: Cancer-Related Analysis of Variants Toolkit David L. Masica1,2, Christopher Douville1,2, Collin Tokheim1,2, Rohit Bhattacharya2,3, RyangGuk Kim4, Kyle Moad4, Michael C. Ryan4, and Rachel Karchin1,2,5 Abstract Cancer sequencing studies are increasingly comprehensive and level interpretation, including joint prioritization of all nonsilent well powered, returning long lists of somatic mutations that can be mutation consequence types, and structural and mechanistic visu- difficult to sort and interpret. Diligent analysis and quality control alization. Results from CRAVAT submissions are explored in an can require multiple computational tools of distinct utility and interactive, user-friendly web environment with dynamic filtering producing disparate output, creating additional challenges for the and sorting designed to highlight the most informative mutations, investigator. The Cancer-Related Analysis of Variants Toolkit (CRA- even in the context of very large studies. CRAVAT can be run on a VAT) is an evolving suite of informatics tools for mutation inter- public web portal, in the cloud, or downloaded for local use, and is pretation that includes mutation mapping and quality control, easily integrated with other methods for cancer omics analysis. impact prediction and extensive annotation, gene- and mutation- Cancer Res; 77(21); e35–38. Ó2017 AACR. Background quickly returning mutation interpretations in an interactive and user-friendly web environment for sorting, visualizing, and An investigator's work is far from over when results are returned inferring mechanism. CRAVAT (see Supplementary Video) is from the sequencing center. Depending on the service, genetic suitable for large studies (e.g., full-exome and large cohorts) mutation calls can require additional mapping to include all and small studies (e.g., gene panel or single patient), performs relevant RNA transcripts or correct protein sequences.
  • Gene Expression Profiling of Corpus Luteum Reveals the Importance Of

    Gene Expression Profiling of Corpus Luteum Reveals the Importance Of

    bioRxiv preprint doi: https://doi.org/10.1101/673558; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Gene expression profiling of corpus luteum reveals the 2 importance of immune system during early pregnancy in 3 domestic sheep. 4 Kisun Pokharel1, Jaana Peippo2 Melak Weldenegodguad1, Mervi Honkatukia2, Meng-Hua Li3*, Juha 5 Kantanen1* 6 1 Natural Resources Institute Finland (Luke), Jokioinen, Finland 7 2 Nordgen – The Nordic Genetic Resources Center, Ås, Norway 8 3 College of Animal Science and Technology, China Agriculture University, Beijing, China 9 * Correspondence: MHL, [email protected]; JK, [email protected] 10 Abstract: The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus 11 the most critical period determining reproductive success. While ovulation rate is the major determinant of 12 litter size in sheep, interactions among the conceptus, corpus luteum and endometrium are essential for 13 pregnancy success. Here, we performed a comparative transcriptome study by sequencing total mRNA from 14 corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 15 crosses, and mapping the RNA-Seq reads to the latest Rambouillet reference genome. A total of 21,287 genes 16 were expressed in our dataset. Highly expressed autosomal genes in the CL were associated with biological 17 processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (eg.
  • Supplemental Information

    Supplemental Information

    Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig.
  • Supp Material.Pdf

    Supp Material.Pdf

    Simon et al. Supplementary information: Table of contents p.1 Supplementary material and methods p.2-4 • PoIy(I)-poly(C) Treatment • Flow Cytometry and Immunohistochemistry • Western Blotting • Quantitative RT-PCR • Fluorescence In Situ Hybridization • RNA-Seq • Exome capture • Sequencing Supplementary Figures and Tables Suppl. items Description pages Figure 1 Inactivation of Ezh2 affects normal thymocyte development 5 Figure 2 Ezh2 mouse leukemias express cell surface T cell receptor 6 Figure 3 Expression of EZH2 and Hox genes in T-ALL 7 Figure 4 Additional mutation et deletion of chromatin modifiers in T-ALL 8 Figure 5 PRC2 expression and activity in human lymphoproliferative disease 9 Figure 6 PRC2 regulatory network (String analysis) 10 Table 1 Primers and probes for detection of PRC2 genes 11 Table 2 Patient and T-ALL characteristics 12 Table 3 Statistics of RNA and DNA sequencing 13 Table 4 Mutations found in human T-ALLs (see Fig. 3D and Suppl. Fig. 4) 14 Table 5 SNP populations in analyzed human T-ALL samples 15 Table 6 List of altered genes in T-ALL for DAVID analysis 20 Table 7 List of David functional clusters 31 Table 8 List of acquired SNP tested in normal non leukemic DNA 32 1 Simon et al. Supplementary Material and Methods PoIy(I)-poly(C) Treatment. pIpC (GE Healthcare Lifesciences) was dissolved in endotoxin-free D-PBS (Gibco) at a concentration of 2 mg/ml. Mice received four consecutive injections of 150 μg pIpC every other day. The day of the last pIpC injection was designated as day 0 of experiment.