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Dataset EV4. Quantitative result tables for INKA analyses. 

INKA analysis result tables for :
a) K562 chronic myeloid leukemia cells
b) SK-Mel-28 melanoma cells
c) HCC827-ER3 non-small cell lung carcinoma cells; a sub-line of HCC827
d) H2228 non-small cell lung carcinoma cells
e) HCC827 non-small cell lung carcinoma cells; parental line of HCC827-ER3
f) H3255 non-small cell lung carcinoma cells (data from Guo et al, 2008)
g) A204 rhabdomyosarcoma cells (data from Bai et al, 2012)
h) MNNG/HOS osteosarcoma cells (data from Bai et al, 2012)
i) U87 glioblastoma cells (van der Mijn et al, 2014)
j) U87-EGFRvIII glioblastoma cells (data from van der Mijn et al, 2014)
k) U87-EGFRvIII glioblastoma cells treated with erlotinib (data from van der Mijn et al, 2014)
l) Tumor tissue biopsy from a hypopharyngeal cancer patient (Pt23) before treatment
m) Tumor tissue biopsy from a hypopharyngeal cancer patient (Pt23) after two weeks of erlotinib treatment
n) Tumor tissue biopsy from a pancreatic cancer patient (Pt24) before treatment
o) Tumor tissue biopsy from a pancreatic cancer patient (Pt24) after two weeks of erlotinib treatment.

For each given kinase, metrics are given for individual analyses (Kinome, ActLoop, PSP, and NWK), accompanied by kinase-centric and substrate-centric INKA score components (Kin = Kinome + ActLoop, Sub = PSP + NWK), INKA scores (Score = √(Kin*Sub)), relative INKA scores (Rel.Score) and skew parameters indicating relative contribution from kinase-centric versus substrate-centric evidence (Skew = arctan(Sub/Kin)*2/π). Skew ranges from 0 (kinase-centric evidence only) to 1 (substrate-centric evidence only), so that a skew of 0.5 indicates equal contribution.  P-values are derived from sample- and kinase-specific null distributions of INKA scores generated after100,000 iterations of a data randomization protocol (see Materials and Methods).

References:
Guo A, Villén J, Kornhauser J, Lee KA, Stokes MP, Rikova K, Possemato A, Nardone J, Innocenti G, Wetzel R, Wang Y, MacNeill J, Mitchell J, Gygi SP, Rush J, Polakiewicz RD & Comb MJ (2008) Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. U. S. A. 105: 692–7.
Bai Y, Li J, Fang B, Edwards A, Zhang G, Bui M, Eschrich S, Altiok S, Koomen J & Haura EB (2012) Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors. Cancer Res. 72: 2501–11.
van der Mijn JC, Sol N, Mellema W, Jimenez CR, Piersma SR, Dekker H, Schutte LM, Smit EF, Broxterman HJ, Skog J, Tannous BA, Wurdinger T & Verheul HMW (2014) Analysis of AKT and ERK1/2 protein kinases in extracellular vesicles isolated from blood of patients with cancer. J. Extracell. Vesicles 3: 25657.

