Figure 1. The human mutation spectrum.

Slides:

Advertisements

Similar presentations

Genome Browsers Ensembl (EBI, UK) and UCSC (Santa Cruz, California)

Advertisements

Chapter 6 PART II: Concepts in Molecular Biology and Genetics The Human Genome: Implications for the Understanding of Human Disease Companion site for.

From: An open day in the metric space

FIG. 1. Scanning electronic microscope image of the unmodified beads; all the bead samples were identical in appearance and size to the unmodified shown.

Figure 2: Algorithm for detecting early warning signal of a critical transition. From: Detecting tissue-specific early warning signals for complex diseases.

Fig. 1. Schematic overview of diffusion maps embedding

Figure 1. Schematic of the corA leader mRNA

Figure 1 The spatial and temporal distribution of diarrhoea rates

Figure 1. Flow diagram of participants recruited into the study.

Fig. 3 Evolutionary game types as a function of relatedness and synergy where each plot is a different social group size. The payoffs used to generate.

Figure 1 Cumulative chance of pregnancy according to age at initiation of pregnancy seeking. The curves were drawn based on the following assumptions:

Figure 3. CRTC1 directly regulates COX-2 and predicts a positive feedback loop deregulated following LKB1 loss. A) Protein immunoblot showing fold induction.

Figure 1. Gene expression analysis

From: Software applications for flux balance analysis

Figure 1. Joint effect of rs and rs on prostate cancer aggressiveness and reclassification. (A) Joint effect of rs and rs on.

Fig. 1. Neem induces caspase-3 activation and cell death in multiple cancer cell types. ( A ) HCT116 cells were treated with neem for 0, 12, 24 and 36h,

Figure 1. Annotation and characterization of genomic target of p63 in mouse keratinocytes (MK) based on ChIP-Seq. (A) Scatterplot representing high degree.

Fig. 1. — The life cycle of S. papillosus. (A) The life cycle of S

Figure 1 A decision tree diagram for problems and its German correspondences From: Corresponding lexical domains: A new resource for onomasiological.

Figure 1. Logos appearing in the choice experiment

From: Computational methods for identifying miRNA sponge interactions

Fig. 1 Flow of ascertainment of cases with incident childhood IgA vasculitis reported by four sources From: Incidence of IgA vasculitis in children estimated.

Figure 1 (A) Chest computed tomography scans of the patient

Figure 1 Overview of the IMPACT Analysis Pipeline

Figure 1. Overview of median-supplement methods

Figure 1. Overall survival of patients receiving alternative medicine (solid lines) vs conventional cancer treatment (dashed lines). Overall survival of.

Figure 1. Number of CCDS IDs and genes represented in the human (A) and mouse (B) CCDS releases. The X-axis indicates the year in which a CCDS dataset.

Fig. 1 Selection of patients

Figure 1. Academic productivity and high academic income: top earners vs. the rest of academics. The average number of ‘peer-reviewed article equivalents’

Figure 1. Examples of e-cigarette discussions in social media

From: Estimating the Location of World Wheat Price Discovery

Figure 1. Time of initiation of therapeutic hypothermia according to who initiated it. Note the logarithmic scaling of the vertical axis. From: Initiation.

Figure 4. (A) A schematic representation from constructs that include modifications in Flag-TDP-12xQ/N. TDP-12xQ/N F4/L (F147, 149, 229, 231/L); TDP-12xQ/N.

Figure 1. Percentage of trainees is represented on the y-axis for each competency/knowledge item represented in the x-axis. Only Poor/Fair (P/F) ratings.

Figure 1. PARP1 binds to abasic sites and DNA ends as a monomer

Figure 1. Exploring and comparing context-dependent mutational profiles in various cancer types. (A) Mutational profiles of pan-cancer somatic mutations,

Figure 1. (A) Cumulative risk of breast (diamonds) and ovarian (squares) cancer in BRCA1 mutation carriers. (B) Cumulative risk of breast (diamonds) and.

From: Structural database resources for biological macromolecules

Figure 2 Care pathways used by women in Morogoro, Tanzania

Figure 1. Progression-free survival and overall survival for FL/DLBCL patients. From: Clinicobiological features and prognostic impact of diffuse large.

Fig. 5. A GC content and het/nonref-hom ratio relationship for exome regions. B GC content and het/nonref-hom ratio relationship for intron regions. C.

Figure 7 miRNA and mRNA gene expression changes in the Poor Group

Chapter 8 Major Histocompatibility Complex

Figure 1. Patterns of HER2–PET/CT confronted with FDG–PET/CT, Maximum intensity projection. Lesion uptake was considered pertinent when visually higher.

Figure 3. Schematic representation of co-expression networks for BipA, SidD, and Erg11 encoding genes. Genes are represented by circles, with positive.

Genomic alterations in non–small cell lung cancer, breast cancer, and colorectal cancer. Genomic alterations in non–small cell lung cancer, breast cancer,

Volume 18, Issue 9, Pages (February 2017)

Protein folding via binding and vice versa

Figure 1. Generation of the S250F Aadc mutant mice

The Role of Chromosome Domains in Shaping the Functional Genome

Figure 1. (A) The VEGF promoter PQS and scheme of G oxidation to OG, as well as (B) the proposed APE1-dependent pathway ... Figure 1. (A) The VEGF promoter.

Volume 18, Issue 5, Pages (November 2015)

Figure 1. Plasma next-generation sequencing (NGS) assay workflow, comparison of variant allelic fraction with ... Figure 1. Plasma next-generation sequencing.

Volume 155, Issue 4, Pages (November 2013)

Figure 1. BRCA1-associated R-Loop accumulation at a non-coding region upstream of ESR1 locus. (A) Alignment of DRIP-seq ... Figure 1. BRCA1-associated.

RAS Proteins and Their Regulators in Human Disease

Volume 66, Issue 1, Pages e6 (April 2017)

Comparison of proteomics and RNA‐Seq data.

Figure 1. Illustration of DGR systems and their prediction using myDGR

Meigang Gu, Kanagalaghatta R. Rajashankar, Christopher D. Lima

Figure 1 Time-dependent progression of α-synuclein accumulation and aggregation in foetal dopamine nigral grafts. ... Figure 1 Time-dependent progression.

Volume 11, Issue 9, Pages (June 2015)

Figure 1. Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein ... Figure 1. Workflow of the HawkDock.

Fig. 1. The ZNF804A interactome

Qian Cong, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin

Small-Molecule Inhibitors Targeting DNA Repair and DNA Repair Deficiency in Research and Cancer Therapy Sarah R. Hengel, M. Ashley Spies, Maria Spies

Figure 1. The overlap between Ensembl/GENCODE, RefSeq and UniProtKB genes. The number of genes classified as coding in ... Figure 1. The overlap between.

Origins and Impacts of New Mammalian Exons

A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function Lea M.

Genome-wide Functional Analysis Reveals Factors Needed at the Transition Steps of Induced Reprogramming Chao-Shun Yang, Kung-Yen Chang, Tariq M. Rana

Presentation transcript:

Figure 1. The human mutation spectrum. From: Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment Brief Bioinform. 2015;17(5):841-862. doi:10.1093/bib/bbv084 Brief Bioinform | © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com

Figure 2. Examples of the coding (functional) and noncoding (regulatory) variants. (i) Functional variant (Pro33Ser) in RRM2B associated with autosomal recessive progressive external ophthalmoplegia visualized on a protein structure (PDB ID: 2vux; Quaternary assembly is generated using PISA/PDBe). Functional variant (Pro33Ser) is highlighted in red color inside the green circle on chains A (part of loop) and B (part of helix). Visualization was created using UCSF Chimera ( www.cgl.ucsf.edu/chimera ). (ii) Protein domain architectures and functional variants mapped to ii (a) RRM2B and ii (b) ZC3HC1. Ribonuc_red_sm = Ribonucleotide reductase domain; zf = C3HC zinc finger-like domain; Rsm1 = Rsm1-like domain. Functional variants are highlighted using red vertical line. Figure was generated using MyDomains ( http://prosite.expasy.org/mydomains/ ). (iii) Genomic localization of the regulatory variants (a) rs10811661 and (b) rs342293. The location of the variants are highlighted using a vertical red line. Regulatory variant rs10811661 regulated the expression of nearby genes CDKN2A and CDKN2B (highlighted in red boxes). Intergenic variant rs342293 located between FLJ36031 (CCDC71L)-PIK3CG is located in a TFBS of EVI1 that regulates the expression (repress) of PIK3CG. Genomic regions were visualized using Ensembl Genome Browser v. 67. From: Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment Brief Bioinform. 2015;17(5):841-862. doi:10.1093/bib/bbv084 Brief Bioinform | © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com

Figure 3. Proportional Venn diagram of genes with coding variants annotated as polymorphism (Polymorphism, n = 11 527), disease (Disease, n = 2105) and unclassified (Unclassified, n = 1910) in Human polymorphisms and disease mutations index. Percentages of genes shared between the three groups are provided. From: Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment Brief Bioinform. 2015;17(5):841-862. doi:10.1093/bib/bbv084 Brief Bioinform | © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com

Figure 4. Histograms depicting the distribution (in percentage) of: ( A ) unassigned regions and ( B ) LCRs in the human proteome. From: Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment Brief Bioinform. 2015;17(5):841-862. doi:10.1093/bib/bbv084 Brief Bioinform | © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com

Figure 5. Examples of IDRs in human proteins: ( A ) Breast cancer type 1 susceptibility protein (BRCA1), ( B ) Cellular tumor antigen p53 (Oncoprotein p53), ( C ) T-cell surface glycoprotein CD4 (Disprot), ( D ) Secondary structure information (UniProtKB) and ( E ) mutation histogram (COSMIC) of BRCA1 is provided to illustrate mutations in the unstructured regions. From: Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment Brief Bioinform. 2015;17(5):841-862. doi:10.1093/bib/bbv084 Brief Bioinform | © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com

Figure 6. Schematic representation of the impact of functional mutation on protein misfolding, folding, aggregation, domain swapping, macromolecular crowding and protein degradation pathways. Structure of misfolded rat CD2 structure (PDB ID: 1A6P) and normal CD2 (PDB ID: 1HNG) is used for representing misfolded and folded structures. Functional variant is represented using red asterisk. From: Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment Brief Bioinform. 2015;17(5):841-862. doi:10.1093/bib/bbv084 Brief Bioinform | © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com

Figure 7. Three-level schema for annotation of functional variants. From: Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment Brief Bioinform. 2015;17(5):841-862. doi:10.1093/bib/bbv084 Brief Bioinform | © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com