lowess normalization  (Partek)

Journal: Oncotarget

Article Title: Overexpression of the E2F target gene CENPI promotes chromosome instability and predicts poor prognosis in estrogen receptor-positive breast cancer

doi: 10.18632/oncotarget.19131

Figure Lengend Snippet: (A) Normalized CENPI mRNA expression in breast cancer compared to normal breast tissue. Data are derived from studies: [ – , – ]. (B) Normalized CENPI mRNA expression in breast cancer molecular subtypes. Data are derived from studies: [ , ]. (C) Normalized CENPI mRNA expression in breast cancer histological subtypes. Data are derived from studies: [ , , , – ]. (D) Western blots of primary normal (Norm) and breast carcinoma tissue samples with estrogen receptor (ER) and progesterone receptor (PR) status as indicated. (E) Quantification of CENP-I protein levels normalized to GAPDH protein levels in primary breast tumor and control breast tissue samples using the Western blots shown in (D). All p values: t-test.

Article Snippet: For analysis of TCGA breast cancer samples, Agilent level 3 log2 lowess-normalized mRNA expression values were downloaded from the TCGA data portal to compare normalized CENPI mRNA expression levels of normal, tumor and/or breast cancer subtype, as indicated [ ].

Techniques: Expressing, Derivative Assay, Western Blot

Journal: Oncotarget

Article Title: Overexpression of the E2F target gene CENPI promotes chromosome instability and predicts poor prognosis in estrogen receptor-positive breast cancer

doi: 10.18632/oncotarget.19131

Figure Lengend Snippet: (A) Distant metastasis-free survival curves of patients from 24 combined datasets (see Methods). Patients were split into high and low CENPI mRNA expression groups using the median CENPI expression level as the cut-off. P-values: log-rank test. (B-D) Distant metastasis-free, recurrence-free and overall survival curves, respectively, of patients with high and low expression levels of CENPI, determined as previously described . P-values: log-rank test.

Article Snippet: For analysis of TCGA breast cancer samples, Agilent level 3 log2 lowess-normalized mRNA expression values were downloaded from the TCGA data portal to compare normalized CENPI mRNA expression levels of normal, tumor and/or breast cancer subtype, as indicated [ ].

Techniques: Expressing

Journal: Oncotarget

Article Title: Overexpression of the E2F target gene CENPI promotes chromosome instability and predicts poor prognosis in estrogen receptor-positive breast cancer

doi: 10.18632/oncotarget.19131

Figure Lengend Snippet: (A) Mutations identified in 3769 breast cancer samples from 5 datasets (see Methods), as described [ , ]. Each mutation was identified only once. The functional impact of the mutations was assessed as described with all identified mutations predicted to have low (L) or medium (M) impact on protein function. The image was obtained by and modified from and . Scale bar indicates amino acid numbers. (B) CENPI mRNA expression levels in normal control breast tissue and breast carcinomas for CENPI allelic copy number categories, as indicated. Data are derived from the TCGA RNAseq and SNP6 microarray datasets . (C) Sequence logo of the E2F1 DNA binding site with consensus sequence and nucleotide frequencies at each position below . The putative E2F1 DNA binding site in the CENPI promoter, P(CENPI), located from positions -127 to -113 upstream of the CENPI transcription start site, was aligned below and overlaid in black font on the sequence logo above. (D) Normalized CENPI mRNA levels in breast carcinoma samples diploid and with copy number loss of the RB1 allele. P-value: Mann Whitney U test. (E) CENPI mRNA levels compared to inferred E2F1 transcription factor activity, computed as described [ , ]. P-value: Spearman correlation. (F) Chromatin immunoprecipitation (ChIP) using IgG, histone H3-specific (α-H3) and E2F1-specific (α-E2F1) antibodies. PCRs were performed on the CENPI promoter, P(CENPI), and the RRP8 promoter, P(RRP8). IgG and dH 2 O served as negative controls, α-H3 and input served as positive controls and P(RRP8) served as negative control for α-E2F1. (G) Retinoblastoma (RB) pathway showing CENPI as an E2F1 target gene. RB1 loss and, to a lesser extent, CENPI allelic copy number alterations contribute to CENPI overexpression in breast cancer.

Article Snippet: For analysis of TCGA breast cancer samples, Agilent level 3 log2 lowess-normalized mRNA expression values were downloaded from the TCGA data portal to compare normalized CENPI mRNA expression levels of normal, tumor and/or breast cancer subtype, as indicated [ ].

Techniques: Mutagenesis, Functional Assay, Modification, Expressing, Derivative Assay, Microarray, Sequencing, Binding Assay, MANN-WHITNEY, Activity Assay, Chromatin Immunoprecipitation, Negative Control, Over Expression

Journal: Oncotarget

Article Title: Overexpression of the E2F target gene CENPI promotes chromosome instability and predicts poor prognosis in estrogen receptor-positive breast cancer

doi: 10.18632/oncotarget.19131

Figure Lengend Snippet: (A) Bar graph of proliferation-adjusted CENPI mRNA levels in TCGA normal control and breast carcinoma samples. The ratio of CENPI mRNA level divided by MKI67 (KI67) mRNA level (CENPI/KI67) is plotted on the y-axis. P-value: Mann-Whitney U test. (B) Proliferation-adjusted survival curves of TCGA ER+ breast cancer patients. CENPI/KI67 ratios as in (A) were calculated for each sample and patients were split in high and low CENPI/KI67 ratio using the median ratio as a cut-off. P-value: log-rank test. (C-F) Recurrence-free survival curves as in Figure for grade 1, grade 2, grade 3 and basal breast cancer patients, respectively. P-value: log-rank test.

Article Snippet: For analysis of TCGA breast cancer samples, Agilent level 3 log2 lowess-normalized mRNA expression values were downloaded from the TCGA data portal to compare normalized CENPI mRNA expression levels of normal, tumor and/or breast cancer subtype, as indicated [ ].

Techniques: MANN-WHITNEY

Journal: Oncotarget

Article Title: Overexpression of the E2F target gene CENPI promotes chromosome instability and predicts poor prognosis in estrogen receptor-positive breast cancer

doi: 10.18632/oncotarget.19131

Figure Lengend Snippet: (A) Gene expression significance signature plot. The degree of co-expression of each gene with CENPI in TCGA ER+ breast cancers was determined by Pearson correlation and genes were ranked from highest to lowest correlation. The red line indicates the position of the number of CIN70 genes in the list, compared to a theoretical no-correlation line in black. P-value: log-rank test. (B) Scatter plot of CENPI mRNA expression level against the CIN70 score for chromosome instability in ER+ TCGA breast cancer samples. The regression line denotes the sum of least squares fit to the data points. P-value: Pearson correlation. (C) The strength of CENPI as a marker for chromosome instability is benchmarked to the performance of the 70 individual genes that contribute to the CIN70 signature, as determined by the R 2 . Percentiles are indicated on the left. Note that CENPI is not part of the CIN70 signature. (D) Box plot showing CENPI mRNA levels in diploid and aneuploid ER+ breast cancers. Whiskers show 10-90 percentiles. P-value <0.0001 (****), assessed by unpaired t-test. (E) Scatter dot plot comparing CENPI mRNA levels to the number of whole-chromosome gains and losses in ER+ breast tumors. Means with standard deviations are indicated, as well as significance levels as per unpaired t-tests: *, p<0.05; **, p<0.01; ****, p<0.0001. Trend line level of significance is assessed using the F-statistic. (F) Scatter dot plot, as in (E) for chromosome arm gains and losses. The numbers on top indicate with how many other groups in the graph each group shows a statistically significant difference at p<0.05, as per unpaired t-tests. (G) Scatter plot comparing CENPI mRNA level to the number of copy number-altered genes in each breast cancer sample. P-value: Pearson correlation.

Article Snippet: For analysis of TCGA breast cancer samples, Agilent level 3 log2 lowess-normalized mRNA expression values were downloaded from the TCGA data portal to compare normalized CENPI mRNA expression levels of normal, tumor and/or breast cancer subtype, as indicated [ ].

Techniques: Expressing, Marker