Last updated: 2021-03-09

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Knit directory: CLLproteomics_batch13/analysis/

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This is the workflow that generates the data analysis results and figures presented in the manuscript "The Proteome Landscape of Chronic Lymphocytic Leukemia (CLL)" by Meier-Abt and Lu et al. Users can also use the associated source code to reproduce all results and figures in the manuscript.

Section 1: Overview of CLL proteomic dataset

Section 2: Identifying proteins associated disease drivers in CLL

Section 3: Proteomic signatures of trisomy12

Section 4: Proteomic signatures of trisomy19

Section 5: Proteomic signature of IGHV mutation status

Section 6: Proteomic signature of del11q

Section 7: Proteomic signature of SF3B1

Section 8: Identifying proteomic biomarkers drug responses and clinical outcomes

Section 9: Factors affecting STAT2 expression in CLL

Additional analyses

Compare the assocations to outcomes between different batches

html report

Protein buffering effect

Test whether proteins in complexes are less buffered than proteins in complexes

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Differentially expressed proteins in five paired patient samples before and after Ibr treatment

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Analysis of batch 2