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| Status |
Public on Dec 06, 2013 |
| Title |
An Integrated Model of the Transcriptome Landscape of HER2-Positive Breast Cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The goal of our study is to build an integrated transcriptome landscape model for HER2 positive breast tumors and identify the crucial signaling pathways associated with HER2 tumors. Genomic features include, 685 genes that were differentially expressed only in HER2-positive tumors, 102 genes that were alternatively spliced in a pattern that is unique to HER2-positive tumors, and 303 genes that expressed single nucleotide sequence variants (eSNVs) that were unique to HER2-positive tumors. Network analysis was performed to integrate the genomic features into a transcriptome landscape model that identified 12 highly interconnected cellular processes that appear to be critical to the establishment and maintenance of HER2-positive tumors. We observed that integrin signaling was linked to lapatinib sensitivity in vitro and strongly associated with risk of relapse in the NCCTG N9831 adjuvant trastuzumab clinical trial dataset.
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| Overall design |
We analyzed RNA-seq data from a survey panel consisting of 8 benign breast lesions, 8 ER+, 8 triple negative, and 8 HER2-positive primary breast tumors to identify genomic features that were uniquely associated with HER2-positive tumors
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| Contributor(s) |
Kalari KR, Necela BM, Tang X, Lau M, Eckel-Passow JE, Anderson SK, Sun Z, Baheti S, Carr JM, Baker TR, Thompson KJ, Radisky DC, Joseph RW, McLaughlin SA, Chai H, Camille S, Rossell D, Asmann YW, Perez EA, Thompson EA |
| Citation(s) |
24223926 |
| Submission date |
Mar 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Krishna R Kalari |
| E-mail(s) |
kalari.krishna@mayo.edu
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| Organization name |
Mayo Clinic
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| Department |
Department of Biomedical Statistics and Informatics
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| Lab |
Dr Thompson-CancerBiology
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| Street address |
200 1st ST SW
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55901 |
| Country |
USA |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (32)
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| Relations |
| BioProject |
PRJNA193673 |
| SRA |
SRP019936 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45419_raw_counts.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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