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Data sets and query script used in identifying FAM129B as a putative regulator of Wnt/β-catenin signaling using large-scale siRNA screen integrated with phosphoproteomic and bioinformatic analyses.

dataset
posted on 03.06.2013 by William H Conrad, Michael B Major, Michele A Cleary, Marc Ferrer, Brian Roberts, Shane Marine, Namjin Chung, William T Arthur, Andy J Chien, Jason D Berndt, Randall T Moon

Data File 1. Results of a large-scale siRNA screen for Wnt/β-catenin signaling in HT1080 B/R cells. Column a contains the siRNA probe ID. Column b contains the ENTREZ gene ID. Coulnm D shows median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to constitutively expressed renilla. P-value calculated using student's T. if, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP <=2, that gene is classified as a hit. Data File 2. Melanoma-associated genes identified by an NCBI gene search. Data File 3a. Protein target overlaps between the siRNA screen and the phosphoproteomic dataset. Column A contains the official gene symbol for protein target of associated peptide. If, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP <=2, that gene is classified as a hit. Phosphoproteomic Hit defined as a 1.7-fold change in phosphosite intensity as described in Old WM et al. 2009. Gene previously associated with melanoma as identified by biopython code described in the Query Script. % control siRNA = median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to a viability marker. Data File 3b. Protein target overlaps between siRNA dataset and the bioinformatic enrichment. If, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP <=2, that gene is classified as a hit. median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to constitutively expressed renilla. Query Script. Biopython script for identifying disease- or query-associated geneIDs.

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