This repository is the code for bioinformatic analysis of the manuscript "The osteogenic niche is a calcium reservoir of breast cancer bone micrometastases and confers unexpected therapeutic vulnerability". The paper is reviewed and in revison for Cancer Cell.
Codes are generated by Dr. Xiang Zhang, Dr. Lin Tian and Dr. Hai Wang.
Please contact haiw@bcm.edu if you have any questions.
- RNAseq dataset normalization
- RNAarray dataset normalization
- Preparation for Analysis
- Gene Set variation analysis
- Analysis on Breast cancer metastasis
- Apply the same procedures for prostate cancer
- correlation between mef2, nfat, mecp2 and Cx43(GJA1)
- Figure S1: Metastasis-free survival curve on 8-gene NFAT signature expression
- Figure S5: Metastasis-free survival curve on Cx43 expression
- Comparison between IVBLs and orthotopic tumors
- Analysis of GSE29036 in Figure 4E
- Figure 7B and Figure S8C & S8D: use heatmaps to visualize the efficacies of drug treatment in BICA
| Dataset (RData) | Objects | Description |
|---|---|---|
| breast-mets-gse14020.RData (The breast cancer metastases data from GSE14020) | allmets.mn | Data matrix with each row as an Affymetrix U133 probe and each column as a metastasis sample |
| --- | allmets.clps | Data matrix derived from allmets.mn with probes mapped to the same gene averaged into one value. |
| --- | allmets.ann | Annotation of breast cancer metastases containing site of metastasis information . The order of rows (samples) is exactly the same as the order of columns in allmets.clps. |
| CRPC-mets-gse77930.RData (The castration resistance prostate cancer metastasis data from GSE77930 | gse77930 | Data matrix with each row as a probe on microarray and each column as a metastasis sample |
| * Please download all the splitted files (.zip, .z01, .z02, .z03) before unzip | gse77930.clps | Data matrix derived from gse77930 with probes mapped to the same gene averaged into one value. |
| --- | gse77930.ann | Annotation of prostate cancer metastases containing site information . The order of rows (samples) is exactly the same as the order of columns in gse77930.clps. |
| Pre-clinical-model-GSE110451.RData | gse110451.clps | Data matrix derived from gse110451 with each role as a gene and each role as a biological replicate of either in vivo bone lesion or a orthotopic tumor. |
| --- | gse110451.ann | Annotation of sample type (IVBL: in vivo bone lesion, or Ortho: orthotopic tumors). |
| Stromal-cell-with-CC-GSE29036.RData (MSC, myoepithelial cells and fibroblasts co-cultured with various cancer cells) | msc.cc | Data matrix with each row as an Affymetrix U133 probe and each column as a metastasis sample |
| * Please download all the splitted files (.zip, .z01, .z02) before unzip | msc.cc.clps | Data matrix derived from msc.cc with probes mapped to the same gene averaged into one value. |
| --- | msc.cc.ann | Annotation of both parties of cells in each co-culture sample. The order of rows (samples) is exactly the same as the order of columns in msc.cc.clps. |
| mef2 signature.txt | --- | MEF2 signature obtained from Di Giorgio et al., PloS Genetics 2017. |