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Visualizing genomic information across chromosomes with PhenoGram

Daniel Wolfe, Scott Dudek, Marylyn D Ritchie, Sarah A Pendergrass
2013 BioData Mining  
, coupled with genomic location information.  ...  One useful data visualization approach for genomic results is the use of chromosomal ideograms.  ...  information of various kinds coupled with genomic location information [1, 2] .  ... 
doi:10.1186/1756-0381-6-18 pmid:24131735 pmcid:PMC4015356 fatcat:k2f5iqmsargfjboakyh6zu5gfa

Clinical interpretation of CNVs with cross-species phenotype data

Sebastian Köhler, Uwe Schoeneberg, Johanna Christina Czeschik, Sandra C Doelken, Jayne Y Hehir-Kwa, Jonas Ibn-Salem, Christopher J Mungall, Damian Smedley, Melissa A Haendel, Peter N Robinson
2014 Journal of Medical Genetics  
in integrating phenotype information across species and the lack of appropriate software tools.  ...  Results-We show that this scheme leads to significant improvements compared with rankings that do not exploit phenotypic information.  ...  Figure 3 shows the phenogram resulting from phenotype and CNV data of a patient with a large deletion on chromosome 18 and several smaller deletions and duplications.  ... 
doi:10.1136/jmedgenet-2014-102633 pmid:25280750 pmcid:PMC4501634 fatcat:dcxpgg3ihbgbjlat2hup77pkhq

A hybrid approach for de novo human genome sequence assembly and phasing

Yulia Mostovoy, Michal Levy-Sakin, Jessica Lam, Ernest T Lam, Alex R Hastie, Patrick Marks, Joyce Lee, Catherine Chu, Chin Lin, Željko Džakula, Han Cao, Stephen A Schlebusch (+4 others)
2016 Nature Methods  
Despite tremendous progress in genome sequencing, the basic goal of producing phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is  ...  BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.  ...  Genome maps were built by in silico nicking with the enzyme Nt.BspQI. Alignment coordinates were plotted on chromosomes using PhenoGram (http://ritchielab.psu.edu/software/phenogram-downloads).  ... 
doi:10.1038/nmeth.3865 pmid:27159086 pmcid:PMC4927370 fatcat:v2odeufe7fgcjjawxqutxexpxu

Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish

S. C. Doelken, S. Kohler, C. J. Mungall, G. V. Gkoutos, B. J. Ruef, C. Smith, D. Smedley, S. Bauer, E. Klopocki, P. N. Schofield, M. Westerfield, P. N. Robinson (+1 others)
2012 Disease Models & Mechanisms  
chromosomes, which is even partially conserved across species (Al-Shahrour et al., 2010) .  ...  The phenogram was visualized using Cytoscape (Smoot et al., 2011) .  ... 
doi:10.1242/dmm.010322 pmid:23104991 pmcid:PMC3597018 fatcat:6hzjdt42fzexlgq7du6c2q6vjy

Comprehensive Analyses of NAC Transcription Factor Family in Almond (Prunus dulcis) and Their Differential Gene Expression during Fruit Development

Zeeshan Zafar, Sidra Fatima, Muhammad Faraz Bhatti
2021 Plants  
We identified 106 NAC genes in P. dulcis genome and were renamed according to their chromosomal distribution.  ...  This study provides insights into the structure and function of PdNAC along with their role in the fruit development to enhance an understanding of NAC in P. dulcis.  ...  Phylogenetic tree was generated to visualize the tree along with the motifs and gene structure for better understanding of motifs and structure distribution across the subgroups.  ... 
doi:10.3390/plants10102200 pmid:34686009 fatcat:gljez5k4g5ek7nush2s25xdwky

Estimation of genetic divergence in meloidogyne mitochondrial DNA

T O Powers, L J Sandall
1988 Journal of nematology  
The mitochondrial genome of M. arenaria is the most genetically distinct of the four species compared.  ...  M. arenaria shows approximately 2.1-3.1% nucleotide sequence divergence from the mitochondrial genomes of M. javanica, M. incognita, and M. hapla.  ...  The two M. javanica genomes form a Phenogram calculated from p values by the unweighted pair group method, UPGMA.  ... 
pmid:19290247 pmcid:PMC2618847 fatcat:alzhhv4nyrcx3is3phvhp5kvni

Mitochondrial DNA variation and Haldane's rule in the Papilio glaucus and P. troilus species groups

Felix A H Sperling
1993 Heredity  
chromosomes (X effect).  ...  In organisms with heterogametic females, like the Lepidoptera, the deficiencies of hybrid females that are expected on the basis of Haldane's rule should lead to congruence of mtDNA variants with species  ...  The question remains: is it more informative to have an unclear picture of a large part of the genome, or a clear picture of a small part of the genome?  ... 
doi:10.1038/hdy.1993.130 fatcat:5gqgpw3fdra4jkruxfhuxad24q

Genome-Wide Analysis of TIR-NBS-LRR Gene Family in Potato Identified StTNLC7G2 Inducing Reactive Oxygen Species in Presence of Alternaria solani

Namo Dubey, Anjali Chaudhary, Kunal Singh
2022 Frontiers in Genetics  
The study identified a total of 44 genes encoding 60 TNL transcripts with two prominent clusters at chromosome 1 and chromosome 11.  ...  NBS-LRR gene family comprised a very large number of genes; therefore, members of one subfamily TIR-NBS-LRR (TNL) are identified in the present study from Solanum tuberosum genome, followed by their bioinformatics  ...  These TNL genes were graphically portrayed on the chromosome using “PhenoGram” tool of Ritchie Lab (http://visualization.ritchielab.psu.edu/phenograms/plot).  ... 
doi:10.3389/fgene.2021.791055 pmid:35082833 pmcid:PMC8784597 fatcat:4no3m66irvb57l3r6d7imaq2ka

An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily

Ai-Ling Ong, Chee-Keng Teh, Sean Mayes, Festo Massawe, David Ross Appleton, Harikrishna Kulaveerasingam
2020 Plants  
any non-coding RNA that may be associated with them for further studies.  ...  We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map.  ...  The phenogram was build using neighbor-joining (NJ) with 1000 bootstrap iterations and visualized using a phylogenetic tree viewer, namely Figtree (v1.4.4) [63] .  ... 
doi:10.3390/plants9111476 pmid:33152992 fatcat:qo35jo7kxbfjjgc6jqlv4q36qm

IDENTIFYING GENETIC ASSOCIATIONS WITH VARIABILITY IN METABOLIC HEALTH AND BLOOD COUNT LABORATORY VALUES: DIVING INTO THE QUANTITATIVE TRAITS BY LEVERAGING LONGITUDINAL DATA FROM AN EHR

SHEFALI S. VERMA, ANASTASIA M. LUCAS, DANIEL R. LAVAGE, JOSEPH B. LEADER, RAGHU METPALLY, SARATHBABU KRISHNAMURTHY, FREDERICK DEWEY, INGRID BORECKI, ALEXANDER LOPEZ, JOHN OVERTON, JOHN PENN, JEFFREY REID (+3 others)
2016 Biocomputing 2017  
In general, we see a pattern of many more statistically significant associations from patients with high variance in the quantitative lab variables, in comparison with the low variance group across all  ...  We first conducted a genome-wide association study (GWAS) with median values of 25 different clinical laboratory measurements to identify variants from Human Omni Express Exome beadchip data that are associated  ...  Black line indicates genome-wide significance (5e-08) threshold. Figure 4 . 4 Phenogram plot representing pleiotropic associations.  ... 
doi:10.1142/9789813207813_0049 pmid:27897004 fatcat:qpphyw7lgvgbvm5fpb7b5ttnji

Odorant Binding Proteins (OBPs) and Odorant Receptors (ORs) of Anopheles stephensi: Identification and comparative insights

Zeeshan Zafar, Sidra Fatima, Muhammad Faraz Bhatti, Farooq A. Shah, Zack Saud, Tariq M. Butt, Joseph Clifton Dickens
2022 PLoS ONE  
No homology was found with D. melanogaster OBPs and ORs.  ...  Phylogenetic and syntenic analyses were carried out to find homology, and thus the evolutionary relationship between An. stephensi OBPs and ORs with those of An. gambiae, Ae. aegypti and D. melanogaster  ...  Similarly, positions of OR encoding genes on An. stephensi chromosomes were visualized using phenogram.  ... 
doi:10.1371/journal.pone.0265896 pmid:35316281 pmcid:PMC8939812 fatcat:ideckrdb5bbhroerhhw2273evm

Development of a tandem repeat-based multilocus typing system distinguishing Babesia bovis geographic isolates

Agustina Perez-Llaneza, Marina Caballero, Eugenia Baravalle, Maria Mesplet, Juan Mosqueda, Carlos E. Suarez, Ignacio Echaide, Frank Katzer, Gabriela M. Pacheco, Monica Florin-Christensen, Leonhard Schnittger
2010 Veterinary parasitology  
across the whole genome.  ...  The genetic difference between isolates was visualized by constructing a phenogram with Treeview (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html).  ... 
doi:10.1016/j.vetpar.2009.09.021 pmid:19833439 fatcat:vnplksuhafclrkrsrjco5b3d2u

Assessment of Genetic Diversity across differentially adopted rice ecotypes

Sridevi, G1., Raju, B.R2., Mohankumar, M.V2* and Sheshshayee, M, S.
2012 Electronic Journal of Plant Breeding  
Geneticdiversity of naturally adopted upland lines along with few germplasm collections in Karnataka were studied basedon 13 SSR loci on chromosome 1.  ...  Out of 4 upland lines one line (AC-35341) intermixed, with C1 and three lines (PS-229,JBT-37/4 and AC-35310) with C3.  ...  This suggested that upland lines could have more similar genome with respect to chromosome 1 for 13 SSR loci's.  ... 
doaj:fbc976371b104cf88517c6f1090e76e7 fatcat:kloxlzo3tvhlnl262acde4epu4

Identifying and validating the presence of Guanine-Quadruplexes (G4) within the blood fluke parasite Schistosoma mansoni

Holly M Craven, Riccardo Bonsignore, Vasilis Lenis, Nicolo Santi, Daniel Berrar, Martin Swain, Helen Whiteland, Angela Casini, Karl F Hoffmann
2021 PLoS Neglected Tropical Diseases  
Here, for the first time, we detail the presence of G-quadruplexes (G4) and putative quadruplex forming sequences (PQS) within the Schistosoma mansoni genome.  ...  Accordingly, four S. mansoni chromosomes (chromosomes 2, 3, 5 and 6) are enriched for PQS when compared to the PLOS NEGLECTED TROPICAL DISEASES baseline frequency detected across the whole genome, with  ...  Multiple comparisons found 3 ´-UTRs were enriched with more PQS/mb compared to other features. C) Phenogram detailing localisation of intragenic PQS in each chromosome.  ... 
doi:10.1371/journal.pntd.0008770 pmid:33600427 pmcid:PMC7924807 fatcat:bh5axkmwhndd5omuqfa7ub7wmy

Phenome-wide Association Study Relating Pretreatment Laboratory Parameters With Human Genetic Variants in AIDS Clinical Trials Group Protocols

C. B. Moore, A. Verma, S. Pendergrass, S. S. Verma, D. H. Johnson, E. S. Daar, R. M. Gulick, R. Haubrich, G. K. Robbins, M. D. Ritchie, D. W. Haas
2014 Open Forum Infectious Diseases  
Acknowledgments We are grateful to the many persons with HIV infection who volunteered for ACTG384, A5095, A5142, A5202, and A5128.  ...  Phenogram [32] was used to visualize results for potentially pleiotropic SNPs. GGPlot2 [33] was used to generate Manhattan plots.  ...  Genome-Wide Association Studies (GWAS) explore whether an individual trait (ie, phenotype) is associated with single-nucleotide polymorphisms (SNPs) across the genome.  ... 
doi:10.1093/ofid/ofu113 pmid:25884002 pmcid:PMC4396430 fatcat:lecpzjxxazbdddmfur5zzh24ou
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