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| Status |
Public on Nov 11, 2011 |
| Title |
Gene expression profiles in breast cancer: breast cancer tissues vs. normal breast tissues |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues.
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| Overall design |
Unpaired experiments, breast tumor tissues vs. breast non-tumor tissues. Biological replicates: 8 breast cancer tissue replicates, 8 breast non-tumor tissue replicates.
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| Contributor(s) |
Lian Z, Wang Q, Li W, Zhang A, Wu L |
| Citation(s) |
22581028 |
| Submission date |
Nov 03, 2011 |
| Last update date |
Oct 11, 2016 |
| Contact name |
wang liang |
| E-mail(s) |
wangliangkexue@163.com
|
| Organization name |
BioChainBJ
|
| Street address |
7A North Yongchang Road BDA
|
| City |
Beijing |
| ZIP/Postal code |
100176 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL14550 |
Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Probe Name Version) |
|
| Samples (16)
|
| GSM827075 |
Breast cancer tissue Replicate 4 |
| GSM827076 |
Breast non-cancer tissue Replicate 1 |
| GSM827077 |
Breast non-cancer tissue Replicate 2 |
| GSM827078 |
Breast non-cancer tissue Replicate 3 |
| GSM827079 |
Breast non-cancer tissue Replicate 4 |
| GSM827080 |
Breast cancer tissue Replicate 5 |
| GSM827081 |
Breast cancer tissue Replicate 6 |
| GSM827082 |
Breast cancer tissue Replicate 7 |
| GSM827083 |
Breast cancer tissue Replicate 8 |
| GSM827084 |
Breast non-cancer tissue Replicate 5 |
| GSM827085 |
Breast non-cancer tissue Replicate 6 |
| GSM827086 |
Breast non-cancer tissue Replicate 7 |
| GSM827087 |
Breast non-cancer tissue Replicate 8 |
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| This SubSeries is part of SuperSeries: |
| GSE33450 |
DNA hypermethylation and gene expression in breast cancer: breast cancer tissues vs. normal breast tissues |
|
| Relations |
| BioProject |
PRJNA154301 |
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