Identification of candidate genes within the 1q32 locus.

Slides:

Advertisements

Similar presentations

Date of download: 6/3/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Novel Integrative Methods for Gene Discovery Associated.

Advertisements

Rupp et al. Supplementary Figure 1: Structure of the human troponin T gene Exon 6 Genomic DNA cDNA from mRNA mutation Exon 9 Exon bp Parts of genomic.

A B D C E 5 kb 2 kb Copies per 1,000 GAPDH copies. UL US TRL

by Nancy D. Borson, Martha Q. Lacy, and Peter J. Wettstein

Fig. 8. Recurrent copy number amplification of BRD4 gene was observed across common cancers. Recurrent copy number amplification of BRD4 gene was observed.

Comparison (θ) of the mean dinucleotide variability distribution for (A) genes with MAE vs. Comparison (θ) of the mean dinucleotide variability distribution.

Comparison (R) of the mean observed to expected dinucleotide distribution for (A) genes with MAE vs. Comparison (R) of the mean observed to expected dinucleotide.

Balancing selection characterizes both MAE genes and cell type-specific genes (expressed in either nsc or asl but not in both). Balancing selection characterizes.

A B C Supplementary figure S7

(A) Heat map showing expression changes during in vitro differentiation of nscs to astrocytes. (A) Heat map showing expression changes during in vitro.

Fig. 4. Primary human metastatic melanomas contain CCL21-expressing LECs, and expression of VEGFC positively correlates with hallmarks of tumor inflammation.

Targeting NY-ESO-1 epitopes restricted on multiple MHC alleles broadens the application of TCR gene therapy and makes it robust toward loss of heterozygosity.

Identification of imprinted genes and imprinted DMRs

The evolution of WCI for biological specificity makes organisms more evolvable. The evolution of WCI for biological specificity makes organisms more evolvable.

Underlying mechanisms.

Placement of inferred ancient genome duplications on the phylogeny of Hexapoda. Placement of inferred ancient genome duplications on the phylogeny of Hexapoda.

Bower building. Bower building. (A) Characteristic behavioral patterns associated with pit digging (Upper) and castle bower building (Lower). (B) Average.

Cell-type–specific ERV expression in primary cells.

Mutations and Genetic Abnormalities

Principal component analysis of the GO category composition of all genes in each genome/transcriptome and WGD paralogs. Principal component analysis of.

WCI evolve as organisms become more complex.

Detection of CD38+IgG1+ memory B cells adjacent to contracted GCs

p110-free p85 is present in MEFs and certain murine tissues.

Confocal microscope images of Reelin mRNA detected by in situ hybridization using a biotinylated oligoprobe (base pairs 1264–1311) visualized with fluorescein.

Comparisons of the circulating latent reservoir and rebound viruses.

Vegfa is overexpressed by E11

H3K4me3 pattern association with functionally relevant genes and changes over time. H3K4me3 pattern association with functionally relevant genes and changes.

Transcriptional response to mating in whole A. gambiae females.

In vitro analysis of K107R white adipocytes.

Genome-wide CRISPR screen correctly identifies known regulators of proximal TCR signaling. Genome-wide CRISPR screen correctly identifies known regulators.

Genomic alterations in breast cancer cell line MDA-MB-231.

Copy-number alterations in an archival breast cancer sample.

Identification of genes associated with a gain of prion susceptibility Increased susceptibilities of revertant cell clones R2, R5 and R7 after retinoic.

Analysis of hESC stages of pluripotency.

Volume 133, Issue 6, Pages (December 2007)

miR‐10b locus is hypermethylated in breast cancer. A

Volume 11, Issue 1, Pages (January 2005)

Immunofluorescece analysis of c-src and v-src distribution in wild-type yeast cells. Immunofluorescece analysis of c-src and v-src distribution in wild-type.

Duplication of the MECP2 Region Is a Frequent Cause of Severe Mental Retardation and Progressive Neurological Symptoms in Males Hilde Van Esch, Marijke.

Hypothyroidism represses the expression of T3-posivite targets independently of NCoR1. Hypothyroidism represses the expression of T3-posivite targets independently.

Expression of NCoR1∆ID in PAX8−/− mice does not reverse repression of T3-positive target genes. qPCR on the indicated pituitary (A) and neuronal (B) genes.

Pearson correlation of gene expression identifies distinct groups of male- and female-enriched genes. Pearson correlation of gene expression identifies.

Histone Modifications Associated with Somatic Hypermutation

Identification and characterization of a novel KRAS rearrangement in metastatic prostate cancer. Identification and characterization of a novel KRAS rearrangement.

Fig. 3 CSF1 is expressed in human melanoma.

Peptide release is not impacted by phosphorothioate modification at interface of the P-site and A-site codons. Peptide release is not impacted by phosphorothioate.

Deletion of Srf with a skeletal muscle-specific Cre transgene.

Landscape of genomic alterations in 444 tumors from 429 patients with mCRPC. Landscape of genomic alterations in 444 tumors from 429 patients with mCRPC.

Responses to high Pi diet in Fgfr1-cKO mice.

Tissue-specific transcriptome responses to fasting.

Proposed model of the tumor-suppressive effects of TPL2 in the lung.

The up-regulation of Galnt3 by Pi requires activation of the ERK pathway and induction of Egr1 and Etv5. The up-regulation of Galnt3 by Pi requires activation.

S. cerevisiae–E. coli chimeras have a partially rescued respiration-competent phenotype. S. cerevisiae–E. coli chimeras have a partially rescued respiration-competent.

Consistency of results across images and time.

FtsZ moves bidirectionally around the mature-septal division plane with filament/bundle velocities similar to those determined in nascent FtsZ rings. FtsZ.

Whole-chromosome view of gene density, inverse environmental variation, inverse total variation, and open chromatin signature. Whole-chromosome view of.

(A) Relative expression levels of the top most down-regulated genes in LATS2L breast tumors (TCGA-BRCA dataset, see Fig 1) in the panel of breast cancer.

Fig. 2 Estimate of the neoantigen repertoire in human cancer.

Fig. 3 The rs risk enhancer is a hub for intrachromosomal and interchromosomal interactions. The rs risk enhancer is a hub for intrachromosomal.

A recurrent gain in the VEGFA locus identifying a molecularly distinct tumor subpopulation. A recurrent gain in the VEGFA locus identifying a molecularly.

EGFR and cetuximab sensitivity of SCCUAT

Ki-67 expression is determined by the cell-cycle stage.

Cell lines with aberrant expression of NRG1 are exquisitely sensitive to downregulation of ERBB3 signaling. Cell lines with aberrant expression of NRG1.

Concordance between the genomic landscape identified by whole-exome sequencing of plasma cfDNA and tumor; DNA and recurrence of KDR/VEGFR2 oncogenic mutations.

Targeting GAPLINC decreased CD44 expression and tumor growth in vivo.

Duplication of the MECP2 Region Is a Frequent Cause of Severe Mental Retardation and Progressive Neurological Symptoms in Males Hilde Van Esch, Marijke.

A and B, linearity of the preamplification step shown by a similar expression pattern of ERα mRNA in four breast tumor samples pre– and post–linear amplification.

Identification of RASA1- and NF1-mutated lung cancer cell lines in the CCLE dataset (accessed via the cBioPortal for Cancer Genomics at

PTEN genotype frequently dictates PTEN expression status, but evidence of heterogeneous staining implies polyclonality within some ovarian tumors. PTEN.

Correlation of TAN phenotypes and TIL effector function.

Presentation transcript:

Identification of candidate genes within the 1q32 locus. Identification of candidate genes within the 1q32 locus. (A) Six candidate genes and correlations between genomic clones and tumor thickness in each subset of melanoma. The locus spanning ∼5.0 Mb, with the correlated clone most strongly correlated with tumor thickness (RP11-243M13) in the center, is shown. Six candidate genes are located in this locus. Filled circles represent genomic clones with P values <0.0071 in each subset of melanoma. (B) (Lower) Results of regression analyses of mRNA expression levels and DNA copy numbers obtained by real-time qPCR analyses of six candidate oncogenes within the 1q32 locus are shown in the data table. (Upper) Regression analysis of NUAK2 that has the strongest correlation among the six candidate oncogenes. Each circle represents mRNA expression levels and DNA copy numbers for each cell line. The filled circle indicates mRNA level and DNA copy number of C32 melanoma cells that have a gain within the 1q32 locus; the open circles represent nine other melanoma cell lines listed in SI Appendix, Table S3. Takeshi Namiki et al. PNAS 2011;108:16:6597-6602 ©2011 by National Academy of Sciences