DOCSLIB.ORG

Viewers: This Article Was Reviewed by Lan Hu, Tim Beissbarth and Dimitar Vassilev

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Viewers: This Article Was Reviewed by Lan Hu, Tim Beissbarth and Dimitar Vassilev Polewko-Klim et al. Biology Direct (2018) 13:17 https://doi.org/10.1186/s13062-018-0222-9 RESEARCH Open Access Integration of multiple types of genetic markers for neuroblastoma may contribute to improved prediction of the overall survival Aneta Polewko-Klim1*, Wojciech Lesinski´ 1, Krzysztof Mnich2, Radosław Piliszek2 andWitoldR.Rudnicki1,2,3 Abstract Background: Modern experimental techniques deliver data sets containing profiles of tens of thousands of potential molecular and genetic markers that can be used to improve medical diagnostics. Previous studies performed with three different experimental methods for the same set of neuroblastoma patients create opportunity to examine whether augmenting gene expression profiles with information on copy number variation can lead to improved predictions of patients survival. We propose methodology based on comprehensive cross-validation protocol, that includes feature selection within cross-validation loop and classification using machine learning. We also test dependence of results on the feature selection process using four different feature selection methods. Results: The models utilising features selected based on information entropy are slightly, but significantly, better than those using features obtained with t-test. The synergy between data on genetic variation and gene expression is possible, but not confirmed. A slight, but statistically significant, increase of the predictive power of machine learning models has been observed for models built on combined data sets. It was found while using both out of bag estimate and in cross-validation performed on a single set of variables. However, the improvement was smaller and non-significant when models were built within full cross-validation procedure that included feature selection within cross-validation loop. Good correlation between performance of the models in the internal and external cross-validation was observed, confirming the robustness of the proposed protocol and results. Conclusions: We have developed a protocol for building predictive machine learning models. The protocol can provide robust estimates of the model performance on unseen data. It is particularly well-suited for small data sets. We have applied this protocol to develop prognostic models for neuroblastoma, using data on copy number variation and gene expression. We have shown that combining these two sources of information may increase the quality of the models. Nevertheless, the increase is small and larger samples are required to reduce noise and bias arising due to overfitting. Reviewers: This article was reviewed by Lan Hu, Tim Beissbarth and Dimitar Vassilev. Keywords: Neuroblastoma, Feature selection, Machine learning, Random forest, Copy number variation, Gene expression, Synergy *Correspondence: [email protected] 1Institute of Informatics, University of Białystok, Konstantego Ciołkowskiego 1M, 15-245 Białystok, Poland Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Polewko-Klim et al. Biology Direct (2018) 13:17 Page 2 of 22 Background weight to prediction of minority class for unbalanced data The current study is the answer to the CAMDA Neu- sets. roblastoma Data Integration Challenge (camda.info). The Unfortunately, the predictive power of models mea- goal of the challenge was the exploration of the opportu- sured on the training set was not correlated with the nities given by the availability of different types of molec- predictive power measured on the validation set. Only for ular data for improving prediction of patient survival in models predicting the sex of a patient, correlation between neuroblastoma. the quality of the model measured on the training set and Neuroblastoma is a cancer manifesting in early child- that measured on the validation set was 0.41, which is sta- hood. It displays a heterogeneous clinical course and a tistically significant, if not very high. Nevertheless, this large fraction of patients with neuroblastoma will eventu- endpoint is not clinically interesting and it was used in ally enter metastasis and have a poor outcome. Accurate the study merely as a reference representing a very easy identification of the high-risk group is critical for deliv- modelling target. ering an appropriate targeted therapy [1]. Currently, the For all other clinical endpoints correlations between prognosis is based on clinical stage and age of the patient MCCobtainedincross-validationandMCCobtainedon [2]. However, research towards inclusion and integration validation sets are very small, confined to a small inter- of genomic data with expression profiles and traditional val between -0.1 and 0.11. What is more, the variance clinical data is actively pursued in the field [3]. In partic- of MCC obtained both on training and validation sets ular, the effort towards establishing a connection between was very high. For example, the following results were clinical outcome and gene expression has been recently obtained for the overall survival: the mean MCC on the the subject of a multinational project involving multi- training set and validation set for 60 models was 0.48 ple bioinformatical and analytical laboratories [4], where and 0.46, and 95% confidence interval is (0.46, 0.51) for gene expression profiles of 498 patients were examined the former and (0.45, 0.49) for the latter. The high vari- using both microarrays and RNA sequencing. Within the ance and lack of correlation between predictive power of CAMDA Neuroblastoma Challenge this data has been the models obtained on the training and the validation accompanied with previously generated data relating copy sets precludes definitive statements about overall superi- number variation (CNV) for the subset of patients consist- ority of one classifier over another, including comparison ing of 145 individuals [2, 5–7]. The clinical data was avail- of relative merits of different data sets used to build the able for all patients, including survival time, classification classifiers. to the low- or high-risk subset, as well as sex. Since the main goal of the current study is to examine Most of the data in the challenge was already used in whether integrating multiple lines of experimental evi- the study aiming at comparison of utility of RNA-seq and dence can improve the quality of predictive models, high microarray data sets for prediction of the clinical endpoint confidence in robustness of results is crucial. For this pur- for neuroblastoma. What is more, the goal of the CAMDA pose, we propose a protocol that gives robust results that challenge is a logical extension of goals pursued in that are well correlated between training and validation sets. study. Therefore, the current study is based on general The protocol is based on an extensive cross-validation and methodology proposed by Zhang et al. utilises four methods for selecting informative features However, the detailed analysis of the results obtained used for model building. We apply this protocol to exam- in that study shows that significant modifications in the ine the relative utility of different data sets for predicting methodology are required. In particular, the design of the a single clinical endpoint, namely the overall survival. Zhang et al. did not allow for the robust and reproducible Finally, we apply the same protocol to examine whether estimate of predictive power of different models. The models that utilise informative variables from more than study was performed using a single split of data between one data set have a higher predictive power in compar- training set, used to develop models, and validation set, ison with the models utilising information from a single used for assessing the quality of predictions. Six inde- data set. The protocol includes a feature selection step. pendent groups developed models using data from the Hence, it allows to explore differences and similarities training set, the quality of which was then assessed on between genes selected as most informative from three the validation set. Sixty models using different approaches independent experimental methods. and different sets of variables were built for each of the six different clinical endpoints. The predictive power of each Methods model was also estimated using cross-validation on the The single split of data between training set and valida- training set. The metric of choice was Matthews Correla- tion set is not sufficient for robust estimate of perfor- tion Coefficient (MCC) [8]whichisabalancedmeasure mance of the machine learning model on external data. of the predictive power of a binary classifier. In compar- Modelling procedure that includes variable selection and ison with the simple accuracy measure, it assigns greater model building is prone to overfitting in both steps. The Polewko-Klim et al. Biology Direct (2018) 13:17 Page 3 of 22 variable selection finds variables that are informative due sufficiently
Load more

Recommended publications
  • Mutations in CHMP2B in Lower Motor Neuron Predominant Amyotrophic Lateral Sclerosis (ALS)
    This is a repository copy of Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS). White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/10846/ Article: Cox, L.E., Ferraiuolo, L., Goodall, E.F. et al. (13 more authors) (2010) Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS). Plos One, 5 (3). Art no.e9872. ISSN 1932-6203 https://doi.org/10.1371/journal.pone.0009872 Reuse Unless indicated otherwise, fulltext items are protected by copyright with all rights reserved. The copyright exception in section 29 of the Copyright, Designs and Patents Act 1988 allows the making of a single copy solely for the purpose of non-commercial research or private study within the limits of fair dealing. The publisher or other rights-holder may allow further reproduction and re-use of this version - refer to the White Rose Research Online record for this item. Where records identify the publisher as the copyright holder, users can verify any specific terms of use on the publisher’s website. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Mutations in CHMP2B in Lower Motor Neuron Predominant Amyotrophic Lateral Sclerosis (ALS) Laura E. Cox1, Laura Ferraiuolo1, Emily F. Goodall1, Paul R. Heath1, Adrian Higginbottom1, Heather Mortiboys1, Hannah C. Hollinger1, Judith A. Hartley1, Alice Brockington1, Christine E.
    [Show full text]
  • Plexin A4 (PLXNA4) (NM 181775) Human Tagged ORF Clone Lentiviral Particle Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC206375L2V Plexin A4 (PLXNA4) (NM_181775) Human Tagged ORF Clone Lentiviral Particle Product data: Product Type: Lentiviral Particles Product Name: Plexin A4 (PLXNA4) (NM_181775) Human Tagged ORF Clone Lentiviral Particle Symbol: PLXNA4 Synonyms: FAYV2820; PLEXA4; PLXNA4A; PLXNA4B; PRO34003 Vector: pLenti-C-mGFP (PS100071) ACCN: NM_181775 ORF Size: 1566 bp ORF Nucleotide The ORF insert of this clone is exactly the same as(RC206375). Sequence: OTI Disclaimer: The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. This clone is substantially in agreement with the reference, but a complete review of all prevailing variants is recommended prior to use. More info OTI Annotation: This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on the nature of the gene. RefSeq: NM_181775.2, NP_861440.1 RefSeq Size: 2020 bp RefSeq ORF: 1569 bp Locus ID: 91584 UniProt ID: Q9HCM2 Protein Families: Druggable Genome MW: 58.1 kDa This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 Plexin A4 (PLXNA4) (NM_181775) Human Tagged ORF Clone Lentiviral Particle – RC206375L2V Gene Summary: Coreceptor for SEMA3A.
    [Show full text]
  • Itraq-BASED QUANTITATIVE ANALYSIS of HIPPOCAMPAL POSTSYNAPTIC DENSITY-ASSOCIATED PROTEINS in a RAT CHRONIC MILD STRESS MODEL of DEPRESSION
    Neuroscience 298 (2015) 220–292 iTRAQ-BASED QUANTITATIVE ANALYSIS OF HIPPOCAMPAL POSTSYNAPTIC DENSITY-ASSOCIATED PROTEINS IN A RAT CHRONIC MILD STRESS MODEL OF DEPRESSION X. HAN, a,b,c W. SHAO, a,b,c Z. LIU, a,b,c S. FAN, a,b,c displayed differences in the abundance of several types of J. YU, b,c J. CHEN, b,c R. QIAO, b,c J. ZHOU b,c* AND proteins. A detailed protein functional analysis pointed to a,b,c,d P. XIE * a role for PSD-associated proteins involved in signaling a Department of Neurology, The First Affiliated Hospital, and regulatory functions. Within the PSD, the N-methyl-D-as- Chongqing Medical University, Chongqing, China partate (NMDA) receptor subunit NR2A and its downstream targets contribute to CMS susceptibility. Further analysis b Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China of disease relevance indicated that the PSD contains a com- c plex set of proteins of known relevance to mental illnesses Chongqing Key Laboratory of Neurobiology, Chongqing, China including depression. In sum, these findings provide novel d Department of Neurology, Yongchuan Hospital, Chongqing insights into the contribution of PSD-associated proteins Medical University, Chongqing, China to stress susceptibility and further advance our understand- ing of the role of hippocampal synaptic plasticity in MDD. Ó 2015 IBRO. Published by Elsevier Ltd. All rights reserved. Abstract—Major depressive disorder (MDD) is a prevalent psychiatric mood illness and a major cause of disability and suicide worldwide. However, the underlying pathophys- iology of MDD remains poorly understood due to its hetero- Key words: major depressive disorder, chronic mild stress, genic nature.
    [Show full text]
  • Plexin A4 (PLXNA4) (NM 181775) Human Recombinant Protein – TP761981 | Origene
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP761981 Plexin A4 (PLXNA4) (NM_181775) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Purified recombinant protein of Human plexin A4 (PLXNA4), transcript variant 2,full length, with N-terminal GST and C-terminal His tag, expressed in E. coli, 50ug Species: Human Expression Host: E. coli Tag: N-GST and C-His Predicted MW: 86 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25mM Tris, pH8.0, 150 mM NaCl, 10% glycerol,1% Sarkosyl. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_861440 Locus ID: 91584 UniProt ID: Q9HCM2 RefSeq Size: 2020 Cytogenetics: 7q32.3 RefSeq ORF: 1566 Synonyms: FAYV2820; PLEXA4; PLXNA4A; PLXNA4B; PRO34003 Summary: Coreceptor for SEMA3A. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm (By similarity).[UniProtKB/Swiss-Prot Function] Protein Families: Druggable Genome This product is to be used for laboratory only.
    [Show full text]
  • © 2014 Jonathan Guo-Han Mun
    © 2014 Jonathan Guo-Han Mun HYPOGLYCEMIA-INDUCED CHANGES IN GLUCOSE METABOLISM IN THE HYPOTHALAMUS BY JONATHAN GUO-HAN MUN DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Nutritional Sciences in the Graduate College of the University of Illinois at Urbana-Champaign, 2014 Urbana, Illinois Doctoral Committee: Professor Rodney W. Johnson, Chair Professor J. Lee Beverly, Director of Research Associate Professor Justin S. Rhodes Associate Professor Manabu T. Nakamura ABSTRACT Hypoglycemia is the most common acute complication associated with insulin-dependent diabetes mellitus (Type 1 and advanced Type 2), which affects 300,000-500,000 individuals of all ages in the United States, with 30,000 new cases each year (1). It is characterized by low blood glucose concentration (less than 70 mg/dL or 4 mM) that can be attributed to a mismatch of insulin, food intake, sleep, and physical activity and can result in serious morbidity or death (2). The glucose counterregulatory response is the primary defense against hypoglycemia and involves (A) secretion of epinephrine and glucagon to elevate blood glucose concentration and (B) sympathetic activation to prompt the individual to take action against hypoglycemia through symptoms that include hunger, shaking, rapid heart rate, and sweating (2). Recurrent episodes of hypoglycemia result in failure of the counterregulatory response, which increases the frequency and severity of subsequent hypoglycemia. The underlying physiology by which this occurs is not well understood (3), but changes occurring in the ventromedial hypothalamus (VMH), a brain region that is responsible for initiating the counterregulatory response to hypoglycemia (4) is the most promising target.
    [Show full text]
  • Taqman® Human Protein Kinase Array
    TaqMan® Gene Signature Arrays TaqMan® Human Protein Kinase Array This array is part of a collection of TaqMan® Gene Signature these kinases are from receptor protein-tyrosine kinase (RPTK) Arrays that enable analysis of hundreds of TaqMan® Gene families: EGFR, InsulinR, PDGFR, VEGFR, FGFR, CCK, NGFR, Expression Assays on a micro fluidic card with minimal effort. HGFR, EPHR, AXL, TIE, RYK, DDR, RET, ROS, LTK, ROR and MUSK. The remaining 15 kinases are Ser/Thr kinases from the Protein kinases are one of the largest families of genes in kinase families: CAMKL, IRAK, Lmr, RIPK and STKR. eukaryotes. They belong to one superfamily containing a eukaryotic protein kinase catalytic domain. The ability of kinases We have also selected assays for 26 non-kinase genes in the to reversibly phosphorylate and regulate protein function Human Protein Kinase Array. These genes are involved in signal has been a subject of intense investigation. Kinases are transduction and mediate protein-protein interaction, transcrip- responsible for most of the signal transduction in eukaryotic tional regulation, neural development and cell adhesion. cells, affecting cellular processes including metabolism, References: angiogenesis, hemopoiesis, apoptosis, transcription and Manning, G., Whyte, D.B., Martinez, R., Hunter, T., and differentiation. Protein kinases are also involved in functioning Sudarsanam, S. 2002. The Protein Kinase Complement of the of the nervous and immune systems, in physiologic responses Human Genome. Science 298:1912–34. and in development. Imbalances in signal transduction due to accumulation of mutations or genetic alterations have Blume-Jensen, P. and Hunter, T. 2001. Oncogenic kinase been shown to result in malignant transformation.
    [Show full text]
  • PRODUCT SPECIFICATION Prest Antigen PLXNA4 Product Datasheet
    PrEST Antigen PLXNA4 Product Datasheet PrEST Antigen PRODUCT SPECIFICATION Product Name PrEST Antigen PLXNA4 Product Number APrEST94436 Gene Description plexin A4 Alternative Gene DKFZp434G0625PRO34003, FAYV2820, KIAA1550, PLXNA4A, PLXNA4B Names Corresponding Anti-PLXNA4 (HPA075592) Antibodies Description Recombinant protein fragment of Human PLXNA4 Amino Acid Sequence Recombinant Protein Epitope Signature Tag (PrEST) antigen sequence: LNAGSNVVVMFGKQPCLFHRRSPSYIVCNTTSSDEVLEMKVSVQVDRAKI HQDLVFQYVEDPTIVRIEPEWSIVSGNTPIAVW Fusion Tag N-terminal His6ABP (ABP = Albumin Binding Protein derived from Streptococcal Protein G) Expression Host E. coli Purification IMAC purification Predicted MW 27 kDa including tags Usage Suitable as control in WB and preadsorption assays using indicated corresponding antibodies. Purity >80% by SDS-PAGE and Coomassie blue staining Buffer PBS and 1M Urea, pH 7.4. Unit Size 100 µl Concentration Lot dependent Storage Upon delivery store at -20°C. Avoid repeated freeze/thaw cycles. Notes Gently mix before use. Optimal concentrations and conditions for each application should be determined by the user. Product of Sweden. For research use only. Not intended for pharmaceutical development, diagnostic, therapeutic or any in vivo use. No products from Atlas Antibodies may be resold, modified for resale or used to manufacture commercial products without prior written approval from Atlas Antibodies AB. Warranty: The products supplied by Atlas Antibodies are warranted to meet stated product specifications and to conform to label descriptions when used and stored properly. Unless otherwise stated, this warranty is limited to one year from date of sales for products used, handled and stored according to Atlas Antibodies AB's instructions. Atlas Antibodies AB's sole liability is limited to replacement of the product or refund of the purchase price.
    [Show full text]
  • “Vesículas Extracelulares De Origen Cerebral Aisladas Desde Suero Presentan Perfil Proteico Diferencial En Dos Modelos De Estrés En Ratas.”
    “Vesículas extracelulares de origen cerebral aisladas desde suero presentan perfil proteico diferencial en dos modelos de estrés en ratas.” Tesis entregada a la Universidad de Chile en cumplimiento de los requisitos para optar al grado de Doctor en Farmacología Facultad de Ciencias Químicas y Farmaceuticas por CRISTÓBAL RAUL GÓMEZ MOLINA Octubre, 2020 DIRECTOR DE TESIS: DRA. ÚRSULA WYNEKEN H. 1 Agradecimientos Quisiera agradecer en primer lugar a mí familia, por el apoyo constante y sostenido en todas las instancias profesionales de mi vida. A mis padres por darme los valores y principios que rigen mi vida. A mi madre, por su fuerza, apoyo incondicional, y amor infinito, que fue capaz de criar a dos hijos cumpliendo el rol de padre y madre a la vez. A mi padre, que, si bien nos acompañó por poco tiempo, logro inculcar en mí el amor por la ciencia y el conocimiento. Y a mi hermana Camila por su alegría y apoyo incondicional. A la Dra. Wyneken, por ser mí guía y tutora, y por la paciencia que tuvo durante este largo proceso. A mis compañeros y amigos del laboratorio de Neurociencias: Soledad, Bárbara, Verónica, Catalina, Ariel, Alejandro, Roberto, Juan Pablo, Carlos, etc., por su apoyo en todo lo que necesité durante este proceso. Agradezco de manera especial a Mauricio, ya que sin su motivación esta tesis no habría llegado a término. A las instituciones que han apoyado la realización de este postgrado, a CONICYT con su beca para estudios de Doctorado en Chile y su beca de apoyo a la realización de la Tesis doctoral.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2013/0330349 A1 Neufeld Et Al
    US 2013 0330349A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0330349 A1 Neufeld et al. (43) Pub. Date: Dec. 12, 2013 (54) HIGHAFFINITY MOLECULES CAPABLE OF Publication Classification BNDING ATYPE A PLEXN RECEPTOR AND USES OF SAME (51) Int. Cl. (75) Inventors: SNEutels,1ryat-11Von as; Noa rRabinoWIcz, E. Kigel, C07K 6/28 (2006.01) Haifa (IL); Asya Varshavsky, Haifa A 6LX39/395 (2006.01) (IL); Ofra Kessler, Haifa (IL) (52) U.S. Cl. (73) Assignee: Rappaport Family Institute for CPC ....... C07K 16/2863 (2013.01); A61K.39/39558 Research in the Medical Sciences, (2013.01) Haifa (IL) USPC ... 424/139.1; 530/387.3: 530/387.9; 435/375 (21) Appl. No.: 14/000,914 (22) PCT Filed: Feb. 23, 2012 (57) ABSTRACT (86). PCT No.: PCT/IL12/SOO57 A high affinity molecule is provided. The high affinity mol S371 (c)(1), ecule comprises a binding domain which binds a type-A (2), (4) Date: Aug. 22, 2013 plexin receptor, wherein said binding domain inhibits prolif Related U.S. Application Data erative signals through said type-A plexin receptor but does (60) Provisional application No. 61/445,567, filed on Feb. not interfere with binding of a neuropilin or semaphorin 6A to 23, 2011. said type-A plexin receptor. Patent Application Publication Dec. 12, 2013 Sheet 1 of 9 US 2013/0330349 A1 à 5 e S s o n ionowolysive,0Povny ked Patent Application Publication Dec. 12, 2013 Sheet 2 of 9 US 2013/0330349 A1 ced S. S. SeO eO WOS80 peue OZ 0,90(S_ o d #007 cy ress O KeGUOld S90% Patent Application Publication Dec.
    [Show full text]
  • Prdc Cdna Insert Product Line
    hPlexin A4 VersaClone cDNA Catalog Number: RDC1214 Specifications: Description This shuttle vector contains the complete ORF for the gene of interest, Gene: hPLXNA4 along with a Kozak consensus sequence for optimal translation initiation. It is inserted NotI to AscI. The gene insert is flanked with Accession: NP_065962 convenient multiple cloning sites which can be used to easily cut and transfer the gene cassette into your desired expression vector. Insert size: 5697bp Preparation and Storage Concentration: 10µg at 0.2μg/μL Formulation cDNA is provided in 10 mM Tris-Cl, pH 8.5 Shipping Ships at ambient temperature Stability 1 year from date of receipt when stored at -20°C to -80°C Storage Use a manual defrost freezer and avoid repeated hPlexin A4 cDNA freeze-thaw cycles. Plasmid PLXNA4 plexin A4 [ Homo sapiens (human) ] HpaI HindIII SspI BamHI Also known as: PLEXA4; PLXNA4A; BmtI NheI NotI PLXNA4B; FAYV2820; PRO34003 EagI BsiWI Summary: AMP EcoNI PLXNA4 is a member of the Plexin family of semaphorin signal transducers. It is found on sensory, COLE1 PshAI autonomic and motor neurons and oligodendrocytes, plus T cells and RDC1214 dendritic cells. PLXNA4 regulates cell 8431 bps Eco47III migration, activation, and axon XhoI guidance via repulsion. It serves as a PspXI SalI receptor for transmembrane XbaI BssHII NsiI semaphorins, Sema6A and 6B, and AscI hPlexin-A4 (1-1894) as a coreceptor with neuropilin 1 for the secreted semaphorin, Sema3A. NruI SphI Alternatively spliced transcripts AccIII encoding different proteins have been described.
    [Show full text]
  • PRODUCT SPECIFICATION Prest Antigen
    PrEST Antigen PLXNA4 Product Datasheet PrEST Antigen PRODUCT SPECIFICATION Product Name PrEST Antigen PLXNA4 Product Number APrEST87605 Gene Description plexin A4 Alternative Gene DKFZp434G0625PRO34003, FAYV2820, KIAA1550, PLXNA4A, PLXNA4B Names Corresponding Anti-PLXNA4 (HPA052141) Antibodies Description Recombinant protein fragment of Human PLXNA4 Amino Acid Sequence Recombinant Protein Epitope Signature Tag (PrEST) antigen sequence: IRAKHGGKEHINICEVLNATEMTCQAPALALGPDHQSDLTERPEEFGFIL DNVQSLLILNKTNFTYYPNPV Fusion Tag N-terminal His6ABP (ABP = Albumin Binding Protein derived from Streptococcal Protein G) Expression Host E. coli Purification IMAC purification Predicted MW 26 kDa including tags Usage Suitable as control in WB and preadsorption assays using indicated corresponding antibodies. Purity >80% by SDS-PAGE and Coomassie blue staining Buffer PBS and 1M Urea, pH 7.4. Unit Size 100 µl Concentration Lot dependent Storage Upon delivery store at -20°C. Avoid repeated freeze/thaw cycles. Notes Gently mix before use. Optimal concentrations and conditions for each application should be determined by the user. Product of Sweden. For research use only. Not intended for pharmaceutical development, diagnostic, therapeutic or any in vivo use. No products from Atlas Antibodies may be resold, modified for resale or used to manufacture commercial products without prior written approval from Atlas Antibodies AB. Warranty: The products supplied by Atlas Antibodies are warranted to meet stated product specifications and to conform to label descriptions when used and stored properly. Unless otherwise stated, this warranty is limited to one year from date of sales for products used, handled and stored according to Atlas Antibodies AB's instructions. Atlas Antibodies AB's sole liability is limited to replacement of the product or refund of the purchase price.
    [Show full text]
  • Dissertation Submitted to the Combined Faculties for the Natural
    Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Diplom-Biochemiker Johannes Hermle born in: Offenbach a.M., Germany Oral-examination: July 26, 2017 siRNA SCREEN FOR IDENTIFICATION OF HUMAN KINASES INVOLVED IN ASSEMBLY AND RELEASE OF HIV-1 Referees: Prof. Dr. Hans-Georg Kräusslich Prof. Dr. Dirk Grimm ii Meiner Familie iii Summary Summary The replication of the human immunodeficiency virus type 1 (HIV-1) is as yet not fully understood. In particular the knowledge of interactions between viral and host cell proteins and the understanding of complete virus-host protein networks are still imprecise. An integral picture of the hijacked cellular machinery is essential for a better comprehension of the virus. And as a prerequisite, new tools are needed for this purpose. To create such a novel tool, a screening platform for host cell factors was established in this work. The screening assay serves as a powerful method to gain insights into virus-host-interactions. It was specifically tailored to addressing the stage of assembly and release of viral particles during the replication cycle of HIV-1. It was designed to be suitable for both RNAi and chemical compound screening. The first phase of this work comprised the setup and optimization of the assay. It was shown, that it was robust and reliable and delivered reproducible results. As a subsequent step, a siRNA library targeting 724 human kinases and accessory proteins was examined. After the evaluation of the complete siRNA library in a primary screen, all primary hits were validated in a second reconfirmation screen using different siRNAs.
    [Show full text]