NRF1 and NRF1 target genes and aggressive Breast Cancer

[jramo033]

Efrain:

I think we should stick to 3 parents, based on my previous finding. I ran Banjo three times for each group (24 in total) and the maximum number of parents among Markov blanket genes of BC was three; being 2 the mode.

[efrain.gonzalez0]

Below I have attached the results of running the Preprior code on the smallest dataset that Jairo provided me with.

[efrain.gonzalez0]

Below I have attached a few results for the datasets J6, J7, and J8.

[jramo033]

Here I am attaching the GeNIe files for the 8 clusters (Breast cancer subtypes and Ethnicity). These files recreate the best structure obtained from Banjo.

[jramo033]

Additional analysis of NHBTNBC using African American controls. Here the excel file used for Banjo and the GeNIe file

[zgong001]

Please see the attachments.

[zgong001]

The attachment is the overall dataset.

Total

846 subjects (85 control / 761 BC)

WHITE=3

626 subjects (79 control / 373 Luminal A, 83 Luminal B, 17 HER2+ and 74 TNBC)

BLACK=2

144 subjects (6 control / 69 Luminal A, 14 Luminal B, 7 HER2+ and 48 TNBC)

Luminal A=0, Luminal B=1, HER2+=2 and TNBC=3

485 Luminal A, 107 Luminal B, 32 HER2+ and 137 TNBC



NRF1 plus most correlated with ethnicity genes (18 genes)

1. Case / control for {Luminal A, Luminal B, HER2,TNBC } in White and Black

2. TNBC {White, Asian} x {Hispanic, Black}

3. Luminal A {White, Asian, Hispanic, Black} x {rest}

4. Luminal B {White, Asian, Hispanic, Black} x {rest}

5. HER2 {White, Asian, Hispanic, Black} x {rest}

[zgong001]

For the analysis 1 of above Breast Cancer Analysis: 1. Case / control for {Luminal A, Luminal B, HER2,TNBC } in White and Black, the attachments are the sub-datasets. The datasets are {Luminal A+control, Black}, {Luminal A+control, White}, {Luminal B+control, Black}, {Luminal B+control, White}, {HER2+control, Black}, {HER2+control, White}, {TNBC +control, Black}, {TNBC +control, White} and the 18 genes which is most correlative with the diseases.

[zgong001]

For the analysis 1 of above Breast Cancer Analysis: 1. Case / control for {Luminal A, Luminal B, HER2,TNBC } in White and Black, the attachments are the sub-datasets. The datasets are {Luminal A+control, Black}, {Luminal A+control, White}, {Luminal B+control, Black}, {Luminal B+control, White}, {HER2+control, Black}, {HER2+control, White}, {TNBC +control, Black}, {TNBC +control, White} and the 18 genes which is most correlative with the diseases.

Updated the disease = 1, no disease =0.

[zgong001]

For the analysis 2 of above Breast Cancer Analysis: 2. TNBC {White, Asian} x {Hispanic, Black}, the attachments are the sub-datasets. The datasets are {TNBC, pairwised(Hispanic, Asian, Black, White)}, and the 18 genes which is most correlative with the ETHNICITY.