Data Analysis for : Diverse Genes with Germline Variants Converging on p53 Network May Predispose to Solid Tumors in Children, Adolescents, and Young Adults
- This github dir contains the data analysis jupyter notebooks, scripts and data tables accompaning the paper :
Diverse Genes with Germline Variants Converging on p53 Network May Predispose to Solid Tumors in Children, Adolescents, and Young Adults- GermLine Analysis of Children, Adolescents, and Young Adults (C-AYA) with SolidTumor
- Authors :
Sara Akhavanfard, Roshan Padmanabhan, Lamis Yehia, Feixiong Cheng, Charis Eng
Contents
IVA Filteration Parameters
Analysis
Known Cancer Predisposing Genes (KCPG)
- KCPG_woAR_Oncoplot
- KCPG_Heatmap
- KCPG_LollipopPlots
- KCPG_woAR_TT-AdrenocorticalCarcinoma_Oncoplot
- KCPG_woAR_TT-Carcinoma_Oncoplot
- KCPG_woAR_TT-CentralNervousSystem_Oncoplot
- KCPG_woAR_TT-EwingsSarcoma_Oncoplot
- KCPG_woAR_TT-GermCellTumor_Oncoplot
- KCPG_woAR_TT-HighGradeGlioma_Oncoplot
- KCPG_woAR_TT-LowGradeGlioma_Oncoplot
- KCPG_woAR_TT-Neuroblastoma_Oncoplot
- KCPG_woAR_TT-Osteosarcoma_Oncoplot
- KCPG_woAR_TT-OtherSolidTumor_Oncoplot
- KCPG_woAR_TT-Retinoblastoma_Oncoplot
- KCPG_woAR_TT-Rhabdomyosarcoma_Oncoplot
- KCPG_woAR_TT-SoftTissueSarcoma_Oncoplot
- KCPG_woAR_TT-Wilmstumor_Oncoplot
Candidate Genes
- CandidateGenes_Oncoplot
- CandidateGenes_Heatmap
- CandidateGenes_LollipopPlots
- CandidateGenes_TT-AdrenocorticalCarcinoma_Oncoplot
- CandidateGenes_TT-Carcinoma_Oncoplot
- CandidateGenes_TT-CentralNervousSystem_Oncoplot
- CandidateGenes_TT-EwingsSarcoma_Oncoplot
- CandidateGenes_TT-GermCellTumor_Oncoplot
- CandidateGenes_TT-HighGradeGlioma_Oncoplot
- CandidateGenes_TT-LowGradeGlioma_Oncoplot
- CandidateGenes_TT-Neuroblastoma_Oncoplot
- CandidateGenes_TT-Osteosarcoma_Oncoplot
- CandidateGenes_TT-OtherSolidTumor_Oncoplot
- CandidateGenes_TT-Retinoblastoma_Oncoplot
- CandidateGenes_TT-Rhabdomyosarcoma_Oncoplot
- CandidateGenes_TT-SoftTissueSarcoma_Oncoplot
- CandidateGenes_TT-Wilmstumor_Oncoplot
C-AYA Patiants with solid tumors vs NonTCGA-ExAC controls
Congential Heart Defects (CHD) Related Genes / Variants
Scripts
- includes inhouse scipts to process and anlayze the data
Data
- table dir contain the supplimentary excel files
- Browse the data at SRA RunSelector
- Summary List for project PRJNA559601 here