Outlier kinase expression by RNA sequencing as targets for precision therapy.

PubWeight™: 1.13‹?› | Rank: Top 10%

🔗 View Article (PMC 3597439)

Published in Cancer Discov on February 05, 2013

Authors

Vishal Kothari1, Iris Wei, Sunita Shankar, Shanker Kalyana-Sundaram, Lidong Wang, Linda W Ma, Pankaj Vats, Catherine S Grasso, Dan R Robinson, Yi-Mi Wu, Xuhong Cao, Diane M Simeone, Arul M Chinnaiyan, Chandan Kumar-Sinha

Author Affiliations

1: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.

Articles citing this

Kras as a key oncogene and therapeutic target in pancreatic cancer. Front Physiol (2014) 1.19

Ret inhibition decreases growth and metastatic potential of estrogen receptor positive breast cancer cells. EMBO Mol Med (2013) 1.07

Adaptive reprogramming of the breast cancer kinome. Clin Pharmacol Ther (2014) 0.88

Not just gRASping at flaws: finding vulnerabilities to develop novel therapies for treating KRAS mutant cancers. Cancer Sci (2014) 0.82

Monocarbonyl curcumin analogues: heterocyclic pleiotropic kinase inhibitors that mediate anticancer properties. J Med Chem (2013) 0.80

RNA-Seq accurately identifies cancer biomarker signatures to distinguish tissue of origin. Neoplasia (2014) 0.80

Basal-like and triple-negative breast cancers: searching for positives among many negatives. Surg Oncol Clin N Am (2014) 0.79

JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2-Targeted Therapies. Cancer Res (2016) 0.76

Aiming for the outliers: cancer precision medicine through targeting kinases with extreme expression. Cancer Discov (2013) 0.75

Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling. Mol Cell Proteomics (2016) 0.75

A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts. Oncotarget (2016) 0.75

KAOS: a new automated computational method for the identification of overexpressed genes. BMC Bioinformatics (2016) 0.75

Articles cited by this

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science (1987) 49.88

Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med (2001) 44.67

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science (2005) 39.06

The protein kinase complement of the human genome. Science (2002) 35.36

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51

Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature (2005) 19.56

ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (2004) 17.08

Efficacy and safety of trastuzumab as a single agent in first-line treatment of HER2-overexpressing metastatic breast cancer. J Clin Oncol (2002) 13.81

Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A (2008) 11.86

Transcriptome sequencing to detect gene fusions in cancer. Nature (2009) 11.63

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (2007) 10.74

Targeting cancer with small molecule kinase inhibitors. Nat Rev Cancer (2009) 9.26

A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell (2009) 8.64

Pancreatic cancer. Annu Rev Pathol (2008) 6.96

Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell (2009) 6.55

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol (2011) 6.54

A gene expression signature associated with "K-Ras addiction" reveals regulators of EMT and tumor cell survival. Cancer Cell (2009) 6.23

Oncogene addiction. Cancer Res (2008) 5.66

Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30

Amplification of AKT2 in human pancreatic cells and inhibition of AKT2 expression and tumorigenicity by antisense RNA. Proc Natl Acad Sci U S A (1996) 4.39

Expressed pseudogenes in the transcriptional landscape of human cancers. Cell (2012) 4.22

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med (2011) 4.10

Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics (2010) 4.07

Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat Rev Clin Oncol (2011) 4.02

Targeting the cancer kinome through polypharmacology. Nat Rev Cancer (2010) 3.74

Oncogenic KRAS activates hedgehog signaling pathway in pancreatic cancer cells. J Biol Chem (2007) 2.34

COPA--cancer outlier profile analysis. Bioinformatics (2006) 2.26

Overexpression of ErbB2 in cancer and ErbB2-targeting strategies. Oncogene (2000) 2.19

A peptidomimetic inhibitor of farnesyl:protein transferase blocks the anchorage-dependent and -independent growth of human tumor cell lines. Cancer Res (1995) 2.04

Treating ALK-positive lung cancer--early successes and future challenges. Nat Rev Clin Oncol (2012) 1.97

The combination of epidermal growth factor receptor inhibitors with gemcitabine and radiation in pancreatic cancer. Clin Cancer Res (2008) 1.68

Molecular consequences of silencing mutant K-ras in pancreatic cancer cells: justification for K-ras-directed therapy. Mol Cancer Res (2005) 1.57

Inactivation of Akt by the epidermal growth factor receptor inhibitor erlotinib is mediated by HER-3 in pancreatic and colorectal tumor cell lines and contributes to erlotinib sensitivity. Mol Cancer Ther (2006) 1.52

Locally advanced pancreatic cancer: current therapeutic approach. Oncologist (2006) 1.39

Pancreatic cancer: from molecular pathogenesis to targeted therapy. Cancer Metastasis Rev (2008) 1.38

Isolation of DNA sequences amplified at chromosome 19q13.1-q13.2 including the AKT2 locus in human pancreatic cancer. Biochem Biophys Res Commun (1996) 1.28

Simultaneous targeting of the epidermal growth factor receptor and cyclooxygenase-2 pathways for pancreatic cancer therapy. Mol Cancer Ther (2005) 1.18

Challenges and opportunities in defining the essential cancer kinome. Sci Signal (2009) 1.05

Treating cancer's kinase 'addiction'. Nat Med (2004) 1.05

Personalized cancer medicine: era of promise and progress. Nat Rev Clin Oncol (2011) 0.84

Antisense oligonucleotides specific to mutated K-ras genes inhibit invasiveness of human pancreatic cancer cell lines. Pancreatology (2001) 0.84

Enhanced therapeutic effects for human pancreatic cancer by application K-ras and IGF-IR antisense oligodeoxynucleotides. World J Gastroenterol (2008) 0.83

The definition of locally advanced pancreatic cancer. Br J Cancer (2010) 0.77

Articles by these authors

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science (2005) 39.06

Identification of pancreatic cancer stem cells. Cancer Res (2007) 18.36

The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature (2002) 18.30

ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (2004) 17.08

Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79

EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci U S A (2003) 13.68

Phenotypic characterization of human colorectal cancer stem cells. Proc Natl Acad Sci U S A (2007) 13.58

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinformatics (2009) 13.34

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature (2009) 12.58

The mutational landscape of lethal castration-resistant prostate cancer. Nature (2012) 11.82

Transcriptome sequencing to detect gene fusions in cancer. Nature (2009) 11.63

Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature (2007) 10.94

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (2007) 10.74

Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res (2004) 9.99

TEAD mediates YAP-dependent gene induction and growth control. Genes Dev (2008) 9.88

Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A (2004) 9.42

Integrative molecular concept modeling of prostate cancer progression. Nat Genet (2006) 8.49

TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res (2006) 7.61

Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science (2008) 7.59

Autoantibody signatures in prostate cancer. N Engl J Med (2005) 7.56

Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res (2002) 7.29

Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09

An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell (2010) 6.76

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol (2011) 6.54

The emergence of lncRNAs in cancer biology. Cancer Discov (2011) 6.32

TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. Am J Surg Pathol (2007) 6.09

Recurrent gene fusions in prostate cancer. Nat Rev Cancer (2008) 6.08

Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell (2005) 6.04

A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell (2007) 5.99

Role of the TMPRSS2-ERG gene fusion in prostate cancer. Neoplasia (2008) 5.92

Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program. Cancer Res (2004) 5.88

Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med (2011) 5.82

DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer. N Engl J Med (2015) 5.39

Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30

EML4-ALK fusion lung cancer: a rare acquired event. Neoplasia (2008) 5.22

alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer. JAMA (2002) 5.07

TMPRSS2:ETV4 gene fusions define a third molecular subtype of prostate cancer. Cancer Res (2006) 4.99

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med (2010) 4.81

Integrative analysis of the cancer transcriptome. Nat Genet (2005) 4.44

Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer. Cancer Cell (2007) 4.43

Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer. Cancer Res (2003) 4.30

Expressed pseudogenes in the transcriptional landscape of human cancers. Cell (2012) 4.22

Probabilistic model of the human protein-protein interaction network. Nat Biotechnol (2005) 3.99

Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat Genet (2013) 3.96

A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. Cancer Res (2007) 3.82

Multiplex biomarker approach for determining risk of prostate-specific antigen-defined recurrence of prostate cancer. J Natl Cancer Inst (2003) 3.73

Antibody-based detection of ERG rearrangement-positive prostate cancer. Neoplasia (2010) 3.66

Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 gene fusions in prostate cancer. Cancer Res (2008) 3.59

Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst (2008) 3.55

Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell (2011) 3.53

Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov (2011) 3.43