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Journal articles on the topic 'Identification of novel genes'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

Qi, Peng-Fei, Yu-Ming Wei, Qing Chen, Thérèse Ouellet, Jia Ai, Guo-Yue Chen, Wei Li, and You-Liang Zheng. "Identification of novel α-gliadin genes." Genome 54, no. 3 (March 2011): 244–52. http://dx.doi.org/10.1139/g10-114.

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Ten novel α-gliadin genes (Gli-ta, Gli-turg1, Gli-turg2, Gli-turg3, Gli-turg4, Gli-turg5, Gli-turg6, Gli-cs1, Gli-cs2, and Gli-cs3) with unique characteristics were isolated from wheat ( Triticum aestivum L.), among which Gli-cs1, Gli-cs2, Gli-cs3, and Gli-turg6 were pseudogenes. Gli-cs3 and nine other sequences were much larger and smaller, respectively, than the typical α-gliadins. This variation was caused by insertion or deletion of the unique domain I and a polyglutamine region, possibly the result of illegitimate recombination. Consequently, Gli-cs3 contained 10 cysteine residues, whereas there were 2 cysteine residues only in the other nine sequences. Gli-ta/Gli-ta-like α-gliadin genes are normally expressed during the development of seeds. SDS–PAGE analysis showed that in-vitro-expressed Gli-ta could form intermolecular disulphide bonds and could be chain extenders. A protein band similar in size to Gli-ta has been observed in seed extracts, and mass spectrometry results confirm that the band contains small molecular mass α-gliadins, which is a characteristic of the novel α-gliadins. Mass spectrometry results also indicated that the two cysteine residues of Gli-ta/Gli-ta-like proteins participated in the formation of intermolecular disulphide bonds in vivo.

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2

Koti, Madhuri, Galina Kataeva, and Azad K. Kaushik. "Identification of novel bovine DH genes." Veterinary Immunology and Immunopathology 128, no. 1-3 (March 2009): 211. http://dx.doi.org/10.1016/j.vetimm.2008.10.006.

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3

Zhao, Liang, Faisal Al Owaidi, Diwakar R. Pattabiraman, Emily Verrier, Anna Tsykin, Gregory J. Goodall, Paul Leo, and Thomas J. Gonda. "Identification of Novel MYB Target Genes." Blood 112, no. 11 (November 16, 2008): 3580. http://dx.doi.org/10.1182/blood.v112.11.3580.3580.

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Abstract The MYB oncogene encodes a transcription factor, Myb, which is essential for normal haemopoiesis and also for the proliferation of most acute leukaemias (reviewed in ref. 1). While a number of Myb target genes have been reported previously, these do not completely account for key elements of MYB’s activity, including its pro-leukaemic and differentiation-suppressing functions. We hypothesised that this reflects the fact that previous screens may have not been sufficiently comprehensive and/or employed the most appropriate cell systems. Thus we have embarked upon a program to identify and validate Myb targets critical for these functions. Here we report results from extensive expression profiling studies using a conditionally myb-transformed myeloid cell line, ERMYB (2). We have used ~44,000-element Illumina Beadchips in conjunction with a kinetic profiling strategy that selects candidates based on rapid, statistically-significant and consistent responses to both activation and inactivation of Myb. This has resulted in the identification of a substantial number of candidate Myb-activated and -repressed genes (381 and 502, respectively). In addition, we have used this cell system to identify candidate Myb-regulated microRNAs. Inspection of the list of candidate Myb-activated genes revealed several previously-described Myb targets including myc, bcl2, gstm1 and mpo, providing additional confidence in our approach. Our focus to date has been on novel candidates that may mediate myb’s ability to enhance proliferation, suppress differentiation and possibly suppress apoptosis. Q-RT-PCR was used as an initial validation step for a number of such targets; to date 13/14 genes identified by array screening have been confirmed by this method in ERMYB cells. A second approach to validation is to confirm correlation with Myb over-expression in a second cell system (FDB-1) (3). As in primary cells, enforced Myb expression can suppress differentiation and promote proliferation of these cells in the presence of GM-CSF (4). Amongst the Myb-activated genes are gfi1 and nucleostemin/gnl3, which are involved in stem-cell functions, cellular proliferation and in the case of gfi1, lineage-specific functions. Strikingly, candidate Myb-repressed genes include several important positive regulators of haemopoietic differentiation and/or negative regulators of proliferation, namely gata3, sfpi1/pu.1, cebpb, junb, klf’s-3,-6 -13 and btg1. Most of these genes have evolutionarily conserved internal or proximal candidate Myb binding sites. Our progress in validating these by chromatin immunoprecipitation will be presented. Finally, we have identified a number of microRNAs that are potentially regulated by Myb. These include members of the miR-17–92 cluster and mir-146b, which appear to be activated and repressed by Myb, respectively. These have been validated by Q-PCR for both the mature miR and the precursor pri-miR transcript. Interestingly, the mir-17–92 cluster has been strongly implicated in oncogenesis and cell cycle regulation (5), while miR-146a/b may have tumour suppressor activity.

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Mirams, Michiko, Babatunde A. Ayodele, Liliana Tatarczuch, Frances M. Henson, Charles N. Pagel, and Eleanor J. Mackie. "Identification of novel osteochondrosis- Associated genes." Journal of Orthopaedic Research 34, no. 3 (September 8, 2015): 404–11. http://dx.doi.org/10.1002/jor.23033.

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5

Liu, Anna Chang, Junmeng Yang, Tina Yuan, and Yongsheng Bai. "Computational Identification of Novel Missense Variants in Coding Regions of Genes Associated with Intellectual Disability." International Journal of Bioscience, Biochemistry and Bioinformatics 11, no. 2 (April 2021): 22–33. http://dx.doi.org/10.17706/ijbbb.2021.11.2.22-33.

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6

Savory, Joanne G. A., Caitlin Edey, Bradley Hess, Alan J. Mears, and David Lohnes. "Identification of novel retinoic acid target genes." Developmental Biology 395, no. 2 (November 2014): 199–208. http://dx.doi.org/10.1016/j.ydbio.2014.09.013.

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7

Lafrenière, Ronald G., and Guy A. Rouleau. "Identification of Novel Genes Involved in Migraine." Headache: The Journal of Head and Face Pain 52 (October 2012): 107–10. http://dx.doi.org/10.1111/j.1526-4610.2012.02237.x.

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8

Hofsli, E., T. E. Wheeler, M. Langaas, A. Lægreid, and L. Thommesen. "Identification of novel neuroendocrine-specific tumour genes." British Journal of Cancer 99, no. 8 (September 30, 2008): 1330–39. http://dx.doi.org/10.1038/sj.bjc.6604565.

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9

Östlund, Gabriel, Mats Lindskog, and Erik L. L. Sonnhammer. "Network-based Identification of Novel Cancer Genes." Molecular & Cellular Proteomics 9, no. 4 (December 3, 2009): 648–55. http://dx.doi.org/10.1074/mcp.m900227-mcp200.

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10

Knowles, Margaret A. "Identification of novel bladder tumour suppressor genes." Electrophoresis 20, no. 2 (February 1, 1999): 269–79. http://dx.doi.org/10.1002/(sici)1522-2683(19990201)20:2<269::aid-elps269>3.0.co;2-7.

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11

Laterza, Omar F., Vijay R. Modur, Dan L. Crimmins, Jitka V. Olander, Yvonne Landt, Jin-Moo Lee, and Jack H. Ladenson. "Identification of Novel Brain Biomarkers." Clinical Chemistry 52, no. 9 (September 1, 2006): 1713–21. http://dx.doi.org/10.1373/clinchem.2006.070912.

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Abstract Background: The diagnosis of diseases leading to brain injury, such as stroke, Alzheimer disease, and Parkinson disease, can often be problematic. In this study, we pursued the discovery of biomarkers that might be specific and sensitive to brain injury. Methods: We performed gene array analyses on a mouse model to look for biomarkers that are both preferentially and abundantly produced in the brain. Via bioinformatics databases, we identified the human homologs of genes that appeared abundant in brain but not in other tissues. We then confirmed protein production of the genes via Western blot of various tissue homogenates and assayed for one of the markers, visinin-like protein 1 (VLP-1), in plasma from patients after ischemic stroke. Results: Twenty-nine genes that were preferentially and abundantly expressed in the mouse brain were identified; of these 29 genes, 26 had human homologs. We focused on 17 of these genes and their protein products on the basis of their molecular characteristics, novelty, and/or availability of antibodies. Western blot showed strong signals in brain homogenates for 13 of these proteins. Tissue specificity was tested by Western blot on a human tissue array, and a sensitive and quantitative sandwich immunoassay was developed for the most abundant gene product observed in our search, VLP-1. VLP-1 was detected in plasma of patients after stroke and in cerebrospinal fluid of a rat model of stroke. Conclusions: The use of relative mRNA production appears to be a valid method of identifying possible biomarkers of tissue injury. The tissue specificity suggested by gene expression was confirmed by Western blot. One of the biomarkers identified, VLP-1, was increased in a rat model of stroke and in plasma of patients after stroke. More extensive, prospective studies of the candidate biomarkers identified appear warranted.

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12

Khalaj, Vahid, Lyndsay Smith, Jayne Brookman, and Danny Tuckwell. "Identification of a novel class of annexin genes." FEBS Letters 562, no. 1-3 (February 27, 2004): 79–86. http://dx.doi.org/10.1016/s0014-5793(04)00186-3.

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13

Gillombardo, C. Barton, Motoo Yamauchi, Mark D. Adams, Jesse Dostal, Sam Chai, Michael W. Moore, Lucas M. Donovan, Fang Han, and Kingman P. Strohl. "Identification of novel mouse genes conferring posthypoxic pauses." Journal of Applied Physiology 113, no. 1 (July 1, 2012): 167–74. http://dx.doi.org/10.1152/japplphysiol.01394.2011.

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Although central to the susceptibility of adult diseases characterized by abnormal rhythmogenesis, characterizing the genes involved is a challenge. We took advantage of the C57BL/6J (B6) trait of hypoxia-induced periodic breathing and its absence in the C57BL/6J-Chr 1A/J/NaJ chromosome substitution strain to test the feasibility of gene discovery for this abnormality. Beginning with a genetic and phenotypic analysis of an intercross study between these strains, we discovered three quantitative trait loci (QTLs) on mouse chromosome 1, with phenotypic effects. Fine-mapping reduced the genomic intervals and gene content, and the introgression of one QTL region back onto the C57BL/6J-Chr 1A/J/NaJ restored the trait. mRNA expression of non-synonymous genes in the introgressed region in the medulla and pons found evidence for differential expression of three genes, the highest of which was apolipoprotein A2, a lipase regulator; the apo a2 peptide fragment (THEQLTPLVR), highly expressed in the liver, was expressed in low amounts in the medulla but did not correlate with trait expression. This work directly demonstrates the impact of elements on mouse chromosome 1 in respiratory rhythmogenesis.

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14

Yoshida, Hideki, Mitsuru Miyachi, Kazutaka Ouchi, Yasumichi Kuwahara, Kunihiko Tsuchiya, Tomoko Iehara, Eiichi Konishi, Akio Yanagisawa, and Hajime Hosoi. "Identification ofCOL3A1andRAB2Aas novel translocation partner genes ofPLAG1in lipoblastoma." Genes, Chromosomes and Cancer 53, no. 7 (April 4, 2014): 606–11. http://dx.doi.org/10.1002/gcc.22170.

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15

Ma, Yihong, Rhonda Croxton, Ronnie L. Moorer, and W. Douglas Cress. "Identification of Novel E2F1-Regulated Genes by Microarray." Archives of Biochemistry and Biophysics 399, no. 2 (March 2002): 212–24. http://dx.doi.org/10.1006/abbi.2002.2761.

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16

Schwiebert, Lisa M., Jeffrey L. Mooney, Stephanie Van Horn, Anirudh Gupta, and Robert P. Schleimer. "Identification of Novel Inducible Genes in Airway Epithelium." American Journal of Respiratory Cell and Molecular Biology 17, no. 1 (July 1997): 106–13. http://dx.doi.org/10.1165/ajrcmb.17.1.2775.

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17

Basham, B., M. Sathe, J. Grein, T. McClanahan, A. D'Andrea, E. Lees, and A. Rascle. "In vivo identification of novel STAT5 target genes." Nucleic Acids Research 36, no. 11 (May 28, 2008): 3802–18. http://dx.doi.org/10.1093/nar/gkn271.

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18

Garbom, Sara, Åke Forsberg, Hans Wolf-Watz, and Britt-Marie Kihlberg. "Identification of Novel Virulence-Associated Genes via Genome Analysis of Hypothetical Genes." Infection and Immunity 72, no. 3 (March 2004): 1333–40. http://dx.doi.org/10.1128/iai.72.3.1333-1340.2004.

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ABSTRACT The sequencing of bacterial genomes has opened new perspectives for identification of targets for treatment of infectious diseases. We have identified a set of novel virulence-associated genes (vag genes) by comparing the genome sequences of six human pathogens that are known to cause persistent or chronic infections in humans: Yersinia pestis, Neisseria gonorrhoeae, Helicobacter pylori, Borrelia burgdorferi, Streptococcus pneumoniae, and Treponema pallidum. This comparison was limited to genes annotated as hypothetical in the T. pallidum genome project. Seventeen genes with unknown functions were found to be conserved among these pathogens. Insertional inactivation of 14 of these genes generated nine mutants that were attenuated for virulence in a mouse infection model. Out of these nine genes, five were found to be specifically associated with virulence in mice as demonstrated by infection with Yersinia pseudotuberculosis in-frame deletion mutants. In addition, these five vag genes were essential only in vivo, since all the mutants were able to grow in vitro. These genes are broadly conserved among bacteria. Therefore, we propose that the corresponding vag gene products may constitute novel targets for antimicrobial therapy and that some vag mutants could serve as carrier strains for live vaccines.

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19

Makalowska, Izabela, Raman Sood, Mezbah U. Faruque, Ping Hu, Christiane M. Robbins, Erica M. Eddings, Juanita D. Mestre, Andreas D. Baxevanis, and John D. Carpten. "Identification of six novel genes by experimental validation of GeneMachine predicted genes." Gene 284, no. 1-2 (February 2002): 203–13. http://dx.doi.org/10.1016/s0378-1119(01)00897-6.

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20

Rahman, Sajida, and Michael F. Miles. "Identification of novel ethanol-sensitive genes by expression profiling." Pharmacology & Therapeutics 92, no. 2-3 (November 2001): 123–34. http://dx.doi.org/10.1016/s0163-7258(01)00163-2.

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21

Pericak-Vance, M. A., J. Grubber, L. R. Bailey, D. Hedges, S. West, L. Santoro, B. Kemmerer, et al. "Identification of Novel Genes in Late-Onset Alzheimer's Disease." Experimental Gerontology 35, no. 9-10 (December 2000): 1343–52. http://dx.doi.org/10.1016/s0531-5565(00)00196-0.

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22

QI, Peng-fei, Yu-ming WEI, Ouellet Thérèse, Qing CHEN, Zhao WANG, Zhen-zhen WEI, and You-liang ZHENG. "Identification of a Group of Novel γ-Gliadin Genes." Journal of Integrative Agriculture 13, no. 2 (February 2014): 290–98. http://dx.doi.org/10.1016/s2095-3119(13)60358-5.

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23

Lickert, Heiko, Doris Kinzel, Ingo Burtscher, Dietrich Truembach, Karsten Boldt, and Marius Ueffing. "Identification and analysis of novel Spemann/Mangold organizer genes." Developmental Biology 319, no. 2 (July 2008): 485. http://dx.doi.org/10.1016/j.ydbio.2008.05.066.

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24

Carvajal-Gamez, B., R. Arroyo, R. Lira, C. López-Camarillo, and M. E. Alvarez-Sánchez. "Identification of two novel Trichomonas vaginalis eif-5a genes." Infection, Genetics and Evolution 10, no. 2 (March 2010): 284–91. http://dx.doi.org/10.1016/j.meegid.2009.12.008.

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25

Xu, B., L. Lin, and N. S. Rote. "Identification of novel genes involved in BeWo cell differentiation." Placenta 19, no. 7 (September 1998): A37. http://dx.doi.org/10.1016/s0143-4004(98)91186-9.

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26

Luedi, P. P., F. S. Dietrich, J. R. Weidman, J. M. Bosko, R. L. Jirtle, and A. J. Hartemink. "Computational and experimental identification of novel human imprinted genes." Genome Research 17, no. 12 (December 1, 2007): 1723–30. http://dx.doi.org/10.1101/gr.6584707.

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27

Fujiwara, Tohru, Hideo Harigae, Shinichiro Takahashi, Kazumichi Furuyama, Mitsuo Kaku, Shigeru Sassa, and Takeshi Sasaki. "Identification of Novel Heme-Regulated Genes during Erythroid Differentiation." Blood 104, no. 11 (November 16, 2004): 1580. http://dx.doi.org/10.1182/blood.v104.11.1580.1580.

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Abstract (Introduction) During erythroid differentiation, a large amount of heme is synthesized for hemoglobin formation. Besides its fundamental role as an oxygen carrier, heme is known to play a key role in transcriptional regulation of certain genes and in translational control of protein synthesis. Since it is known that both the level of erythroid-specific genes and heme content increase together during erythroid differentiation, heme may likely regulate the expression of erythroid-specific genes. It is also possible that heme might regulate even a wider variety of genes than hemoglobin synthesis in cells undergoing erythroid differentiation. With this view in mind, we have searched for novel genes that are under the control of heme. For this purpose, we used the wild-type and heme-deficient erythroblasts generated from the wild-type and ALAS2 (-) ES cells in vitro and compared their gene expression profiles. By this approach, we have identified and reported four novel erythroid-specific genes previously (ASH meeting 2003). In the present study, we have further investigated the mechanisms of heme-mediated regulation of these genes. (Methods) cDNA sequences of these genes were determined by 5′RACE and data-base search. In order to generate erythroblasts containing various amounts of heme, ALAS2 (-) ES subclones, which had been partially rescued by human ALAS2 cDNA driven under the erythroid-specific promoter, were established and induced to undergo erythroid differentiation. Correlation between the level of expression of these genes and intracellular heme content was examined. In addition, the promoter region of one of these genes, NuSAP, was cloned, and its cis-element, through which heme regulates the expression, was determined by promoter analysis and EMSA. (Results) The level of expression of all these genes was closely correlated with intracellular heme content in the partially rescued ALAS2 (-) erythroblasts, indicating that expression of these genes is clearly under the control of heme. The results of 5′-RACE and database search have allowed us to identify that these genes consist of uncoupling protein2 (UCP2), nucleolar spindle-associated protein (NuSAP) and two as yet uncharacterized genes (EST1 and 2). While EST1 consists of 110 a.a. with a GK motif which is characteristic of acetyltransferase, EST2 consists of 972 a.a, with nucleotide sequence indicative of a serine/threonine kinase with a putative transmembrane domain. In order to determine the heme regulatory motif, we also performed the promoter analysis of the NuSAP gene. The results showed that CCAAT box, located 34 nucleotides upstream from the transcription initiation site, was essential for the promoter activity, and the binding activity of a protein complex to this element was enhanced in DMSO-treated MEL cells, suggesting that heme regulates the expression of the NuSAP gene through this motif. (Conclusion) These results demonstrate that expression of a wide variety of genes, which may have quite different functions from hemoglobin formation, may also be regulated by heme in erythroid cells undergoing cell differentiation.

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28

HANLON, P., W. ZHENG, A. KO, and C. JEFCOATE. "Identification of novel TCDD-regulated genes by microarray analysis." Toxicology and Applied Pharmacology 202, no. 3 (February 1, 2005): 215–28. http://dx.doi.org/10.1016/j.taap.2004.06.018.

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29

Graham, Michelle A., Kevin A. T. Silverstein, Steven B. Cannon, and Kathryn A. VandenBosch. "Computational Identification and Characterization of Novel Genes from Legumes." Plant Physiology 135, no. 3 (July 2004): 1179–97. http://dx.doi.org/10.1104/pp.104.037531.

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30

Resmini, E., B. Morte, E. Sorianello, E. Gallardo, N. de Luna, I. Illa, A. Zorzano, J. Bernal, and S. Webb. "Identification of Novel GH-regulated Genes in C2C12 Cells." Hormone and Metabolic Research 43, no. 13 (November 9, 2011): 919–30. http://dx.doi.org/10.1055/s-0031-1291285.

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31

Klasberg, Steffen, Tristan Bitard-Feildel, and Ludovic Mallet. "Computational Identification of Novel Genes: Current and Future Perspectives." Bioinformatics and Biology Insights 10 (January 2016): BBI.S39950. http://dx.doi.org/10.4137/bbi.s39950.

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32

LaGier, M. J., and D. S. Threadgill. "Identification of novel genes in the oral pathogenCampylobacter rectus." Oral Microbiology and Immunology 23, no. 5 (October 2008): 406–12. http://dx.doi.org/10.1111/j.1399-302x.2008.00443.x.

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33

Lung, M. S., A. Trainer, and I. Campbell. "Identification of novel CRC pathway genes in familial CRC." Annals of Oncology 27 (October 2016): vi2. http://dx.doi.org/10.1093/annonc/mdw362.07.

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34

Takamatsu, K. "Identification of Two Novel Primate-Specific Genes in DSCR." DNA Research 9, no. 3 (January 1, 2002): 89–97. http://dx.doi.org/10.1093/dnares/9.3.89.

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35

Lowe, Adrian M., David T. Beattie, and Robert L. Deresiewicz. "Identification of novel staphylococcal virulence genes byin vivoexpression technology." Molecular Microbiology 27, no. 5 (March 1998): 967–76. http://dx.doi.org/10.1046/j.1365-2958.1998.00741.x.

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36

Wang, X. Z. "Identification of novel stress-induced genes downstream of chop." EMBO Journal 17, no. 13 (July 1, 1998): 3619–30. http://dx.doi.org/10.1093/emboj/17.13.3619.

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37

Lagos-Quintana, M. "Identification of Novel Genes Coding for Small Expressed RNAs." Science 294, no. 5543 (October 26, 2001): 853–58. http://dx.doi.org/10.1126/science.1064921.

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Ersahin, Tulin, Levent Carkacioglu, Tolga Can, Ozlen Konu, Volkan Atalay, and Rengul Cetin-Atalay. "Identification of Novel Reference Genes Based on MeSH Categories." PLoS ONE 9, no. 3 (March 28, 2014): e93341. http://dx.doi.org/10.1371/journal.pone.0093341.

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39

Kiryu, Sumiko, Gui Lan Yao, and Hiroshi Kiyama. "Identification of novel genes expressed during hypoglossal nerve regeneration." Neuroscience Research Supplements 19 (January 1994): S146. http://dx.doi.org/10.1016/0921-8696(94)92676-x.

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40

Patrzykat, Aleksander, Jeffrey W. Gallant, Jung-Kil Seo, Jennifer Pytyck, and Susan E. Douglas. "Novel Antimicrobial Peptides Derived from Flatfish Genes." Antimicrobial Agents and Chemotherapy 47, no. 8 (August 2003): 2464–70. http://dx.doi.org/10.1128/aac.47.8.2464-2470.2003.

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ABSTRACT We report on the identification of active novel antimicrobials determined by screening both the genomic information and the mRNA transcripts from a number of different flatfish for sequences encoding antimicrobial peptides, predicting the sequences of active peptides from the genetic information, producing the predicted peptides chemically, and testing them for their activities. We amplified 35 sequences from various species of flatfish using primers whose sequences are based on conserved flanking regions of a known antimicrobial peptide from winter flounder, pleurocidin. We analyzed the sequences of the amplified products and predicted which sequences were likely to encode functional antimicrobial peptides on the basis of charge, hydrophobicity, relation to flanking sequences, and similarity to known active peptides. Twenty peptides were then produced synthetically and tested for their activities against gram-positive and gram-negative bacteria and the yeast Candida albicans. The most active peptide (with the carboxy-terminus amidated sequence GWRTLLKKAEVKTVGKLALKHYL, derived from American plaice) showed inhibitory activity over a concentration range of 1 to 8 μg/ml against a test panel of pathogens, including the intrinsically antibiotic-resistant organism Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and C. albicans. The methods described here will be useful for the identification of novel peptides with good antimicrobial activities.

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41

McNair, Katelyn, Carol Zhou, Elizabeth A. Dinsdale, Brian Souza, and Robert A. Edwards. "PHANOTATE: a novel approach to gene identification in phage genomes." Bioinformatics 35, no. 22 (April 25, 2019): 4537–42. http://dx.doi.org/10.1093/bioinformatics/btz265.

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Abstract Motivation Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path. Results We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank’s non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes. Availability and implementation https://github.com/deprekate/PHANOTATE Supplementary information Supplementary data are available at Bioinformatics online.

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42

Daya, Michelle, and Kathleen C. Barnes. "Identification of novel allergic diathesis genes: Are we closer to novel therapeutic targets?" Journal of Allergy and Clinical Immunology 143, no. 2 (February 2019): 557–59. http://dx.doi.org/10.1016/j.jaci.2018.11.028.

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43

Serrado Marques, José, Vera Teixeira, António Jacinto, and Ana Tavares. "Identification of Novel Hemangioblast Genes in the Early Chick Embryo." Cells 7, no. 2 (January 31, 2018): 9. http://dx.doi.org/10.3390/cells7020009.

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Wang, Peng, Jie Zhao, and Ann K. Corsi. "Identification of novel target genes of CeTwist and CeE/DA." Developmental Biology 293, no. 2 (May 2006): 486–98. http://dx.doi.org/10.1016/j.ydbio.2005.10.011.

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Park, Inju, Seong-Eui Hong, Tae-Wan Kim, Jiae Lee, Jungsu Oh, Eunyoung Choi, Cecil Han, Hoyong Lee, Do Han Kim, and Chunghee Cho. "Comprehensive identification and characterization of novel cardiac genes in mouse." Journal of Molecular and Cellular Cardiology 43, no. 2 (August 2007): 93–106. http://dx.doi.org/10.1016/j.yjmcc.2007.05.018.

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Hoff, Andreas M., Sharmini Alagaratnam, Sen Zhao, Jarle Bruun, Peter W. Andrews, Ragnhild A. Lothe, and Rolf I. Skotheim. "Identification of Novel Fusion Genes in Testicular Germ Cell Tumors." Cancer Research 76, no. 1 (December 9, 2015): 108–16. http://dx.doi.org/10.1158/0008-5472.can-15-1790.

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Banu, Sayera, Kaori Ohtani, Harumi Yaguchi, Tint Swe, Stewart T. Cole, Hideo Hayashi, and Tohru Shimizu. "Identification of novel VirR/VirS-regulated genes in Clostridium perfringens." Molecular Microbiology 35, no. 4 (February 2000): 854–64. http://dx.doi.org/10.1046/j.1365-2958.2000.01760.x.

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Soo, Chia, David N. Sayah, Xinli Zhang, Steven R. Beanes, Ichiro Nishimura, Catherine Dang, Earl Freymiller, and Kang Ting. "The Identification of Novel Wound-Healing Genes through Differential Display." Plastic and Reconstructive Surgery 110, no. 3 (September 2002): 787–97. http://dx.doi.org/10.1097/01.prs.0000019717.64418.e6.

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Lee, Jeen Hee, Hidehiro Kondo, Shigeru Sato, Seiji Akimoto, Toshio Saito, Masaaki Kodama, and Shugo Watabe. "Identification of novel genes related to tetrodotoxin intoxication in pufferfish." Toxicon 49, no. 7 (June 2007): 939–53. http://dx.doi.org/10.1016/j.toxicon.2007.01.008.

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MURTHY, ANITA E., ANDRE BERNARDS, DEANNA CHURCH, JOHN WASMUTH, and JAMES F. GUSELLA. "Identification and Characterization of Two Novel Tetratricopeptide Repeat-Containing Genes." DNA and Cell Biology 15, no. 9 (September 1996): 727–35. http://dx.doi.org/10.1089/dna.1996.15.727.

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