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Human breast cancer cell line and tissue, ISE-affinity proteogenomics

ABSTRACT: Introducing a clinical-practical, alternative splicing activity-based proteogenomic method that identifies, in their oncogenically active states, biomarker genes bearing patient-specific GE or copy-number alterations of prognostic significance. This integrated multi-omics method uses intronic splicing enhancers (ISEs) probes to sort in situ ISE-interacting trans-acting protein factors (trans-interactome) directly from a heterogeneous tumor for subsequent mass spectrometry (MS) characterization.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast, Cell Culture, Breast Cancer Cell Line

DISEASE(S): Breast Cancer

SUBMITTER: Li Wang

LAB HEAD: Xian Chen

PROVIDER: PXD008642 | Pride | 2018-03-20

REPOSITORIES: Pride

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			Action	DRS
	AS_RNA10.raw	Raw
	AS_RNA11.raw	Raw
	AS_RNA12.raw	Raw
	AS_RNA13.raw	Raw
	AS_RNA14.raw	Raw

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Publications

Novel RNA-Affinity Proteogenomics Dissects Tumor Heterogeneity for Revealing Personalized Markers in Precision Prognosis of Cancer.

Wang Li L Wrobel John A JA Xie Ling L Li DongXu D Zurlo Giada G Shen Huali H Yang Pengyuan P Wang Zefeng Z Peng Yibing Y Gunawardena Harsha P HP Zhang Qing Q Chen Xian X

Cell chemical biology 20180301 5

To discriminate the patient subpopulations with different clinical outcomes within each breast cancer (BC) subtype, we introduce a robust, clinical-practical, activity-based proteogenomic method that identifies, in their oncogenically active states, candidate biomarker genes bearing patient-specific transcriptomic/genomic alterations of prognostic value. First, we used the intronic splicing enhancer (ISE) probes to sort ISE-interacting trans-acting protein factors (trans-interactome) directly fr ...[more]

PMID: 29503206

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