Supplementary MaterialsFigure S1: CGH hybridization proportion within a tetraploid region in LAU-Me275. ratios, shades the Bibf1120 kinase activity assay Gaussian elements high light. The true variety of components identified as well as the Bayes Information Criterion are indicated in each figure title.(DOC) pone.0018369.s003.doc (67K) GUID:?F58C26DB-7CE5-47D2-8768-DA315179FEBD Body S4: Evaluation of CNV recognition algorithm in CGH data. Sections are, from still left to correct: a melanoma with huge deletions (LAU-Me280); a melanoma with huge amplifications (LAU-Me275); and a control EBV cell collection (male) hybridized using a pool of female references. From top to bottom: CNV classification (following CBS segmentation) using 1) Gaussian Combination Model (GMM), 2) MergeLevels, 3) the scoring-based approach. Each dot corresponds to a CGH probe with its genomic position around the X axis and its log2 ratio of hybridization around the Y axis. Colors indicate the copy number state: orange ?=?1 copy gray?=?2 copies, cyan?=?3 copies and dark blue more than 3 copies. For the scoring approach distinction is made between 1 copy (orange) and 0 copy (reddish).(DOC) pone.0018369.s004.doc (154K) GUID:?D1B83B18-921F-4F5C-A78A-45AA8F545B27 Physique S5: Optimization of Illumina analysis and comparison with Affymetrix prediction in LAU-Me275. A. Pearson correlation between SNP CN, as a function of OverUnder windows size. B. Copy Bibf1120 kinase activity assay number concordance at each SNP for different windows sizes of OverUnder. Colors indicate windows size parameters, the bar height indicates the total quantity of SNPs (in log10 level) found in one replicate. The gray bar indicates the intersection between two technical replicates. The percentage of concordance (quantity of SNPs found with the same copy number bin in both Bibf1120 kinase activity assay replicates/total quantity Bibf1120 kinase activity assay of SNPs from this given copy number bin in the first replicate) is shown on top of each bar. C. Copy number prediction on chromosome 1 using OverUnder with a windows size of 201 SNPs. D. Copy number prediction on chromosome 1 using an Affymetrix 6.0 array (with the PICNIC algorithm).(DOC) pone.0018369.s005.doc (110K) GUID:?3E967CAB-F18E-47CB-98B8-4E56B7C5AE47 Physique S6: Copy number analysis using Illumina SNP arrays. DNA from LAU-Me275 was hybridized to Illumina SNP arrays, and the data were analyzed using the method of Attiyeh et al. The top panel shows genome-wide copy number: dark blue indicates more than three copies; cyan:three copies; gray:copy natural; orange: deletion. Following panels present chromosome 7 with, throughout: Hybridization log2 proportion; B allele regularity; and duplicate amount prediction.(DOC) pone.0018369.s006.doc (134K) GUID:?19D56A1C-9FF6-4460-89DD-936879CBC4Advertisement Body Rabbit polyclonal to ANKRD50 S7: Intersection between CGH and SNP predictions. A. Intersection between SNP and CGH predictions for genes with an increase of than 4 copies. B. Intersection for genes within deletions. C. Intersection for genes within deletions that expression had not been discovered.(DOC) pone.0018369.s007.doc (105K) GUID:?8FB10DFE-3C95-4873-9B8C-82FC7589A625 Figure S8: Duplicate number prediction from CGH and Bibf1120 kinase activity assay SNP arrays, LOH prediction from SNP arrays. (PDF) pone.0018369.s008.pdf (245K) GUID:?B9EC4C2B-CBA9-4E38-92F0-C43E0D6663A7 Figure S9: Boxplots of SILAC large/light normalized log2 ratios. In every tests, LAU-Me275 was tagged using the large isotope; the unlabeled test is certainly indicated in the boxplot label in the X axis. NHM identifies the pool of regular melanocytes and self-self to a control test only using LAU-Me275 to check on for just about any bias because of the label/no label lifestyle circumstances (no significant bias was discovered).(DOC) pone.0018369.s009.doc (66K) GUID:?B36F1BE6-CE18-4A9A-B5B7-C12F61E43863 Figure S10: Histogram of exclusive peptides discovered per protein in the SILAC data. (DOC) pone.0018369.s010.doc (54K) GUID:?116656B9-DB53-4930-9272-E8ECE515B2D5 Figure S11: Relationship between mRNA expression and protein levels. Both SILAC and RNA seq log2 ratios are portrayed for LAU-Me275 with regards to the test indicated in each story title. Spearman Rho correlation coefficient is indicated in the name. In all experiments, the correlation is usually significantly positive (p 0.001).(DOC) pone.0018369.s011.doc (77K) GUID:?7BF51730-5E00-478B-9328-440918CF85CE Table S1: Count of genes affected by SCNA. (DOC) pone.0018369.s012.doc (49K) GUID:?F8B1C950-39D2-4399-AB69-9409C4E1549C Table S2: Processed list of SCNA genes in all seven melanoma cell lines. (XLS) pone.0018369.s013.xls (197K) GUID:?9A706E6E-8641-4063-952B-6F49F0BDA3DF Table S3: Genomic and transcriptomic data for SCNA-genes in all seven melanoma cell lines. (XLS) pone.0018369.s014.xls (929K) GUID:?255FD148-263C-4D66-A454-CF12361B3708 Table S4: List of pathways significantly enriched in SCNA, and pathway comparison between three melanoma datasets..