Human and mouse cancer genome copy number alteration (CNA) conservation

Choose signatures for cross-tumor type or cross-species CNA comparisons.

A .gct file will be generated. This file can be loaded into the Integrative Genome Viewer (IGV) (link) for viewing.
We tend to view the abs_min_consistent and synteny rows as 'bar charts' with 'autoscaling' once opened in IGV - right click on these rows to enable these settings.

Highlighted are the signatures used in the Graham, NA, Minasyan, A, et al. manuscript, (2017):
Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures, Molecular Systems Biology 13 (2): 914.



For more information on included signatures refer to the table below.

Human

Human core signature A tumors

OV - Ovarian serous cystadenocarcinoma
    Top 10% of PC1-based core signature A ovarian serous cystadenocarcinoma tumors

    Ovarian serous cystadenocarcinoma

BRCA - Breast invasive carcinoma
    Top 10% of PC1-based core signature A breast invasive carcinoma tumors

    Breast invasive carcinoma

    Breast invasive carcinoma basal

    Breast invasive carcinoma luminal A B

UCEC - Uterine corpus endometrial carcinoma
    Top 10% of PC1-based core signature A uterine corpus endometrial carcinoma tumors

    Uterine corpus endometrial carcinoma

    Uterine corpus endometrial carcinoma serous and serous like

LU - Lung carcinoma
    Top 10% of PC1-based core signature A lung squamous cell carcinoma and adenocarcinoma tumors

    Lung squamous cell carcinoma

    Lung adenocarcinoma


To submit

Human expanded signature A

    Bladder urothelial carcinoma

    Rectum adenocarcinoma

    Skin cutaneous melanoma

    Colon adenocarcinoma

    Head and neck squamous cell carcinoma


To submit

Human additional signatures

    Stomach adenocarcinoma

    Glioblastoma multiforme

    Prostate adenocarcinoma

    Brain lower grade glioma

    Thyroid carcinoma

    Kidney renal clear cell carcinoma


To submit

Human phenotype scored validation signatures

    Breast invasive carcinoma 18F-fluorodeoxy-glucose


To submit

Mouse

Mouse tissue-matched core signature A

    Mouse model of mammary cancer, GEO accession # GSE30710

    Mouse model of mammary cancer, GEO accession # GSE43997

    Mouse model of mammary cancer, GEO accession # GSE27101


To submit

Mouse tissue-matched expanded signature A

    Mouse epithelial transformed bladder cells, GEO accession # GSE45128

    Mouse model of melanoma cancer, GEO accession # GSE58265

    Mouse epithelial transformed colon cells, GEO accession # GSE70790


To submit

Mouse additional tissue-matched signatures

    Mouse model of glioblastoma/high-grade astrocytoma, GEO accession # GSE22927

    Mouse model of prostate cancer, GEO accession # GSE61382

    Mouse model of prostate cancer, GEO accession # GSE35247

    Mouse epithelial transformed kidney cells, GEO accession # GSE45128


To submit

MEF validation signatures

Signature A mouse embryonic fibroblasts (MEFs)
    Immortalized wildtype mouse embryonic fibroblasts (MEFs) from CD1 mouse strain, GEO accession # GSE63306

    Immortalized mouse embryonic fibroblasts (MEFs) with p53 knock-out from mixed mouse strain, GEO accession # GSE63306

Evolving MEFs
    Immortalized wildtype mouse embryonic fibroblasts (MEFs) from CD1 mouse strain profiled at subsequent passages, GEO accession # GSE63306

Signature B
    Immortalized wildtype mouse embryonic fibroblasts (MEFs) from CD1 mouse strain, GEO accession # GSE63306


To submit

User defined datasets (optional)

    Typically summary CNA signatures (as opposed to individual sample CNA results)




Input file in .gct format indexed on gene names



GCT format
Example GCT file (Human and Mouse).
Human gene names
Mouse gene names

Reference Genome for cross-species comparisons

    Results will be mapped onto the chosen reference genome.





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Reference files:

KEGG Glycolysis & Gluconeogenesis, Pentose Phosphate, and Carbon Fixation enzymes (Regions files for IGV viewer)

HUMAN Glycolysis_PentoseP_CarbonFix_regions_12.6.13_hg19.bed
MOUSE Glycolysis_PentoseP_CarbonFix_regions_12.10.13_mm9.bed

The TCGA pan-cancer PCA loadings for PC1-3 and TCGA tissue-specific PCA loading for PC1-2 with respect to their genomic position

TCGA_pan-cancer_PCA_loadings_for_PC1-3.seg
TCGA_tissue-specific_PCA_loadings_for_PC1-2.seg

MEF PCA loadings for PC1-2 with respect to their genomic position

MEFs_PCA_loadings_for_PC1-2.seg

Abbreviated nameFull nameNumber of samples
TCGA OV signature A (top 10%)Top 10% of PC1-based core signature A ovarian serous cystadenocarcinoma tumors
63
TCGA OVOvarian serous cystadenocarcinoma
584
TCGA BRCA signature A (top 10%)Top 10% of PC1-based core signature A breast invasive carcinoma tumors
87
TCGA BRCABreast invasive carcinoma
873
TCGA BRCA basalBreast invasive carcinoma basal
81
TCGA BRCA luminal A B (sig. B)Breast invasive carcinoma luminal A B
323
TCGA UCEC signature A (top 10%)Top 10% of PC1-based core signature A uterine corpus endometrial carcinoma tumors
50
TCGA UCECUterine corpus endometrial carcinoma
492
TCGA UCEC serous and serous likeUterine corpus endometrial carcinoma serous and serous like
60
TCGA LU signature A (top 10%)Top 10% of PC1-based core signature A lung squamous cell carcinoma and adenocarcinoma tumors
72
TCGA LUSC - lung squamous cell carcinomaLung squamous cell carcinoma
359
TCGA LUAD (sig. B) - lung adenocarcinomaLung adenocarcinoma
368
TCGA BLCA - bladder urothelial carcinomaBladder urothelial carcinoma
97
TCGA READ - rectum adenocarcinomaRectum adenocarcinoma
168
TCGA SKCM - skin cutaneous melanomaSkin cutaneous melanoma
256
TCGA COAD - colon adenocarcinomaColon adenocarcinoma
447
TCGA HNSC - head and neck squamous cell carcinomaHead and neck squamous cell carcinoma
308
TCGA STAD - stomach adenocarcinomaStomach adenocarcinoma
162
TCGA GBM - glioblastoma multiformeGlioblastoma multiforme
593
TCGA PRAD - prostate adenocarcinomaProstate adenocarcinoma
171
TCGA LGG - brain lower grade gliomaBrain lower grade glioma
181
TCGA THCA - thyroid carcinomaThyroid carcinoma
333
TCGA KIRC - kidney renal clear cell carcinomaKidney renal clear cell carcinoma
539
MSKCC BRCA FDG-PET high vs lowBreast invasive carcinoma 18F-fluorodeoxy-glucose
10
Brca #1 - mouse model of mammary cancerMouse model of mammary cancer, GEO accession # GSE30710
57
Brca #2 - mouse model of mammary cancerMouse model of mammary cancer, GEO accession # GSE43997
62
Brca #3 - mouse model of mammary cancerMouse model of mammary cancer, GEO accession # GSE27101
44
Blca - mouse epithelial transformed bladder cellsMouse epithelial transformed bladder cells, GEO accession # GSE45128
6
Skcm - mouse model of melanoma cancerMouse model of melanoma cancer, GEO accession # GSE58265
30
Coad - mouse epithelial transformed colon cellsMouse epithelial transformed colon cells, GEO accession # GSE70790
7
Gbm - mouse model of glioblastoma/high-grade astrocytomaMouse model of glioblastoma/high-grade astrocytoma, GEO accession # GSE22927
72
Prad #1 - mouse model of prostate cancerMouse model of prostate cancer, GEO accession # GSE61382
55
Prad #2 - mouse model of prostate cancerMouse model of prostate cancer, GEO accession # GSE35247
18
Kirc - mouse epithelial transformed kidney cellsMouse epithelial transformed kidney cells, GEO accession # GSE45128
7
Wildtype MEFs signature A (PC1)Immortalized wildtype mouse embryonic fibroblasts (MEFs) from CD1 mouse strain, GEO accession # GSE63306
28
p53-/- MEFs signature A (PC1)Immortalized mouse embryonic fibroblasts (MEFs) with p53 knock-out from mixed mouse strain, GEO accession # GSE63306
37
Wildtype MEFs evolving signature A (paired t-test, mid to late passage)Immortalized wildtype mouse embryonic fibroblasts (MEFs) from CD1 mouse strain profiled at subsequent passages, GEO accession # GSE63306
10
Wildtype MEFs signature B (PC1)Immortalized wildtype mouse embryonic fibroblasts (MEFs) from CD1 mouse strain, GEO accession # GSE63306
15

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References:

Human-mouse cancer genome copy number alteration conservation and mouse embryonic fibroblasts (MEFs, GSE63306)
Graham, NA, Minasyan, A, Lomova, A, Cass, A, Balanis, NG, Friedman, M, Chan, S, Zhao, S, Delgado, A, Go, J, Beck, L, Hurtz, C, Ng, C, Qiao, R, ten Hoeve, J, Palaskas, N, Wu, H, Müschen, M, Multani, AS, Port, E, Larson, SM, Schultz, N, Braas, D, Christofk, HR, Mellinghoff, IK, and Graeber, TG.(2017). Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures. Molecular Systems Biology 13, 914.

TCGA (The Cancer Genome Atlas)
The TCGA aCGH data used in the above signatures was generated by the TCGA Research Network: http://cancergenome.nih.gov/

MSKCC BRCA FDG-PET dataset
Palaskas N, Larson SM, Schultz N, Komisopoulou E, Wong J, Rohle D, Campos C, Yannuzzi N, Osborne JR, Linkov I, Kastenhuber ER, Taschereau R, Plaisier SB, Tran C, Heguy A, Wu H, Sander C, Phelps ME, Brennan C, Port E, Huse JT, Graeber TG, Mellinghoff IK. 18F-Fluorodeoxy-glucose Positron Emission Tomography Marks MYC-Overexpressing Human Basal-Like Breast Cancers. Cancer Res. 2011;71:5164–74.

Mouse models of mammary cancer (GSE30710, GSE43997, GSE27101)
Drost R, Bouwman P, Rottenberg S, Boon U, Schut E, Klarenbeek S, Klijn C, van der Heijden I, van der Gulden H, Wientjens E, Pieterse M, Catteau A, Green P, Solomon E, Morris JR, Jonkers J. BRCA1 RING Function Is Essential for Tumor Suppression but Dispensable for Therapy Resistance. Cancer Cell. 2011;20:797–809.
Herschkowitz JI, Zhao W, Zhang M, Usary J, Murrow G, Edwards D, Knezevic J, Greene SB, Darr D, Troester MA, Hilsenbeck SG, Medina D, Perou CM, Rosen JM. Comparative oncogenomics identifies breast tumors enriched in functional tumor-initiating cells. Proc Natl Acad Sci U S A. 2012;109:2778–83.

Mouse model of melanoma cancer (GSE58265)
Viros A, Sanchez-Laorden B, Pedersen M, Furney SJ, Rae J, Hogan K, Ejiama S, Girotti MR, Cook M, Dhomen N, Marais R. Ultraviolet radiation accelerates BRAF-driven melanomagenesis by targeting TP53. Nature. 2014;511:478–82.

Mouse model of glioblastoma/high-grade astrocytoma (GSE22927)
Chow LML, Endersby R, Zhu X, Rankin S, Qu C, Zhang J, Broniscer A, Ellison DW, Baker SJ. Cooperativity within and among Pten, p53, and Rb pathways induces high-grade astrocytoma in adult brain. Cancer Cell. 2011;19:305–16.

Mouse models of prostate cancer (GSE35247, GSE61382)
Wanjala J, Taylor BS, Chapinski C, Hieronymus H, Wongvipat J, Chen Y, Nanjangud GJ, Schultz N, Xie Y, Liu S, Lu W, Yang Q, Sander C, Chen Z, Sawyers CL, Carver BS. Identifying Actionable Targets through Integrative Analyses of GEM Model and Human Prostate Cancer Genomic Profiling. Mol Cancer Ther. 2015;14:278–88.
Ding Z, Wu C-J, Jaskelioff M, Ivanova E, Kost-Alimova M, Protopopov A, Chu GC, Wang G, Lu X, Labrot ES, Hu J, Wang W, Xiao Y, Zhang H, Zhang J, Zhang J, Gan B, Perry SR, Jiang S, Li L, Horner JW, Wang YA, Chin L, DePinho RA. Telomerase reactivation following telomere dysfunction yields murine prostate tumors with bone metastases. Cell. 2012;148:896–907.

Transformed epithelial murine cells modeling human carcinomas: bladder, kidney and colon (GSE45128, GSE70790)
Padilla-Nash HM, McNeil NE, Yi M, Nguyen Q-T, Hu Y, Wangsa D, Mack DL, Hummon AB, Case C, Cardin E, Stephens R, Difilippantonio MJ, Ried T. Aneuploidy, oncogene amplification and epithelial to mesenchymal transition define spontaneous transformation of murine epithelial cells. Carcinogenesis. 2013;34:1929–39.

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