Data from: High sensitivity isoelectric focusing to establish a signaling biomarker for the diagnosis of human colorectal cancer

Padhan N, Nordling TEM, Sundström M, Åkerud P, Birgisson H, Nygren P, Nelander S, Claesson-Welsh L

Date Published: September 4, 2016

DOI: http://dx.doi.org/10.5061/dryad.h35p4

 

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Title Raw Protein RPAs
Downloaded 20 times
Description The relative peak area (RPA), i.e. peak area value of the 23 different activity levels of the 7 signal transducers after normalization to the HSP70 level analyzed in parallel in each sample (columns 2-24). This file contains one sample per row and one protein per column with the sample name in the first column and the protein name in the first row. Columns 25-27 contain the result of the mutation analysis of KRAS and BRAF. One in column 25 (MutationKRAS) indicate that KRAS is mutated in the sample, one in column 26 (MutationBRAF) indicates that BRAF is mutated, while one in column 27 (Wildtype) indicate that neither KRAS nor BRAF is mutated. A one in the binary variables in column 28-31 indicate the classification of each sample as normal mucosa, colorectal cancer (CRC) stage II, CRC stage IV, or metastasis. NaN is used to indicate that no measurement was done.
Download Padhan BMC Cancer 2016 Raw Protein RPAs.csv (90.11 Kb)
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Title Raw Protein RPAs Constructed features replicate corrected
Downloaded 12 times
Description File shows the relative peak area (RPA), i.e. peak area value of the measured protein after normalization to the HSP70 level analyzed in parallel in each sample (columns 2-24, 28-42). This file contains one sample per row and one protein per column with the sample name in the first column and the protein name in the first row. Column 25-27 contain the result of the mutation analysis of KRAS and BRAF. One in column 25 (MutationKRAS) indicate that KRAS is mutated in the sample, one in column 26 (MutationBRAF) indicates that BRAF is mutated, while one in column 27 (Wildtype) indicate that neither KRAS nor BRAF is mutated. Columns 28 to 42 contain the RPA values of the constructed features, i.e. features that are calculated based on the 23 different activity levels of the 7 signal transducers in column 2-24. The four replicates of each constructed feature contains the minimum, maximum, mean, and median value based on all possible ways to combine the replicates of the proteins used to construct the feature. A one in the binary variables in column 43-46 indicate the classification of each sample as normal mucosa, colorectal cancer (CRC) stage II, CRC stage IV, or metastasis. In the last column the classification is 1 = normal mucosa, 2 = colorectal cancer (CRC) stage II, 3 = CRC stage IV, or 5 = metastasis. NaN is used to indicate that no measurement was done.
Download Padhan BMC Cancer 2016 Raw Protein RPAs C...ed.csv (134.9 Kb)
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Title Padhan BMC Cancer 2016 Supplemental Results
Downloaded 20 times
Description File contains the test statistic (T) for each possible combination of 1-3 features, including the constructed features (column 5 and 6). One combination is shown per row with the name of the feature combination in the first column and the header explaining the value in each column in the first row.
Download Padhan BMC Cancer 2016 Supplemental Results.xlsx (3.616 Mb)
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When using this data, please cite the original publication:

Padhan N, Nordling TEM, Sundström M, Åkerud P, Birgisson H, Nygren P, Nelander S, Claesson-Welsh L (2016) High sensitivity isoelectric focusing to establish a signaling biomarker for the diagnosis of human colorectal cancer. BMC Cancer 16(1): 683. http://dx.doi.org/10.1186/s12885-016-2725-z

Additionally, please cite the Dryad data package:

Padhan N, Nordling TEM, Sundström M, Åkerud P, Birgisson H, Nygren P, Nelander S, Claesson-Welsh L (2016) Data from: High sensitivity isoelectric focusing to establish a signaling biomarker for the diagnosis of human colorectal cancer. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.h35p4
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