Journal: JNCI Journal of the National Cancer Institute

Article Title: Differences in Genomic Profiles and Outcomes Between Thoracic and Adrenal Neuroblastoma

doi: 10.1093/jnci/djz027

Figure Lengend Snippet: Adrenal vs thoracic tumor copy number association analysis. A) Meta-analysis by nonoverlapping 1-Mb tiles. The y-axis reflects an inverse variance-weighted meta-analysis across four datasets—single nucleotide polymorphism (SNP) microarray, whole genome sequencing, whole exome sequencing, and gene panel sequencing cohorts—of average log-ratio (tumor normalized to normal) differences between adrenal vs thoracic cases divided by SD (z score). A positive z score (red) implies that the relative copy number is higher in adrenal vs thoracic cases and a negative z score (blue) implies the opposite. The inner dashed line illustrates the z score corresponding to a nominal P value cut point of .05, and the outer dotted line illustrates the z score corresponding to a multiple test-adjusted false discovery rate (FDR) cut point of 0.05. The 1-Mb bin containing MYCN is labeled, because it is the only focal copy number alteration to reach statistical significance. B) Meta-analysis by chromosome arm. “Avg Adrenal” and “Avg Thoracic” denote a weighted average copy number log-ratio for adrenal and thoracic cases, respectively. More positive/red values reflect regions of greater copy number gain and more negative/blue values reflect regions of greater copy number loss. From the difference of these values (Avg Difference), a z score and two-tailed P value were computed by inverse-variance meta-analysis. The FDR was controlled by the Benjamini-Hochberg method. Results with multiple test-adjusted statistical significance at FDR less than 0.05 are bolded.

Article Snippet: Functional Genomic Associations With Neuroblastoma Site of Origin To evaluate the relationship of primary site with functional subclasses of neuroblastoma, we performed unsupervised hierarchical clustering on adrenal (n = 143) and thoracic (n = 19) cases with RNA expression profiling obtained by HuEx microarray, as well as adrenal (n = 128) and thoracic (N = 15) cases with DNA methylation profiling by Infinium microarray.

Techniques: Microarray, Sequencing, Labeling, Two Tailed Test

Journal: JNCI Journal of the National Cancer Institute

Article Title: Differences in Genomic Profiles and Outcomes Between Thoracic and Adrenal Neuroblastoma

doi: 10.1093/jnci/djz027

Figure Lengend Snippet: Unbiased clustering analysis of functional genomic and DNA methylation data in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) cohort. Heatmaps and hierarchical clustering for all adrenal and thoracic (A) HuEx RNA microarray samples and (B) DNA methylation microarray samples. Rows reflect independent patient profiles and columns reflect the 200 probesets with the highest variance after (A) log2 transformation of RNA probe intensity and (B) logit transformation of methylation beta values. Columns are mean-centered and normalized by SD (z score transformation) and illustrated on a blue-yellow scale. Additional colored boxes illustrate clinical annotations for each patient according to the legend (white = missing annotation).

Article Snippet: Functional Genomic Associations With Neuroblastoma Site of Origin To evaluate the relationship of primary site with functional subclasses of neuroblastoma, we performed unsupervised hierarchical clustering on adrenal (n = 143) and thoracic (n = 19) cases with RNA expression profiling obtained by HuEx microarray, as well as adrenal (n = 128) and thoracic (N = 15) cases with DNA methylation profiling by Infinium microarray.

Techniques: Functional Assay, DNA Methylation Assay, Microarray, Transformation Assay, Methylation

Journal: Orthopaedic Surgery

Article Title: Non‐coding RNA Identification in Osteonecrosis of the Femoral Head Using Competitive Endogenous RNA Network Analysis

doi: 10.1111/os.12834

Figure Lengend Snippet: Differentially expressed genes (DEGs) identification between osteonecrosis of the femoral head (ONFH) and normal samples. The DE‐lncRNAs and DE‐mRNAs between ONFH and normal samples were identified from GSE74089 by limma package in R based on the criteria of with the adjusted P value <0.05 and |log fold change (FC)| ≥2. DE‐miRNAs were identified from GSE89587 on the basis of adjusted P value <0.05. Volcano plots display the distribution of DE‐mRNAs (A), DE‐lncRNAs (C), and DE‐miRNAs (E). The vertical dotted lines in A and C represent |log FC| = 2 and the horizontal dotted lines represent adjusted P value = 0.05. Red spots represent up‐regulated genes and green spots represent down‐regulated genes in ONFH samples compared with normal samples. Hierarchical clustering demonstrates the top 10 DE‐mRNAs (B), DE‐lncRNAs (D), and DE‐miRNAs (F) in descending order by log FC.

Article Snippet: The microarray data of expression profile of GSE74089 (GPL13497) was obtained from the National Center for Biotechnology Information (NCBI) GEO database .

Techniques:

Journal: Scientific Reports

Article Title: Circular RNAs expression profiles in human gastric cancer

doi: 10.1038/s41598-017-09076-6

Figure Lengend Snippet: Hierarchical clustering, volcano plots, and scatter plots exhibited the differentially expressed circRNAs in gastric cancer tissues compared to paired non-gastric cancer tissues. ( A ) Hierarchical clustering, numbers were the samples used for the microarray assay. C: cancer tissues, N: non-cancerous tissues. ( B ) Differentially expressed circRNAs were displayed by volcano plots. The green and red parts indicated >2 fold-decreased and -increased expression of the dysregulated circRNAs in GC tissues, respectively (p < 0.05). ( C ) Differentially expressed circRNAs were displayed by scatter plots. The green and red parts indicated >2 fold-decreased and -increased expression of the dysregulated circRNAs in GC tissues (p < 0.05).

Article Snippet: The circRNAs expression profile microarray chip assay and data and bioinformatics analysis were carried out by Capitalbio Corporation (Beijing, China).

Techniques: Microarray, Expressing

Journal: Scientific Reports

Article Title: Circular RNAs expression profiles in human gastric cancer

doi: 10.1038/s41598-017-09076-6

Figure Lengend Snippet: The top up- and down-regulated differentially expressed circRNAs in GC tissues compared to those in non-cancerous tissues by both probes.

Article Snippet: The circRNAs expression profile microarray chip assay and data and bioinformatics analysis were carried out by Capitalbio Corporation (Beijing, China).

Techniques:

Journal: Scientific Reports

Article Title: Circular RNAs expression profiles in human gastric cancer

doi: 10.1038/s41598-017-09076-6

Figure Lengend Snippet: Verification of the differentially expressed circRNAs by qRT-PCR. The expression of 7 lncRNAs in 50 paired GC tissues was detected by qRT-PCR, which were shown by the expression fold changes. Comparison of the results obtained from qPCR and microarray assay revealed satisfactory consistency.

Article Snippet: The circRNAs expression profile microarray chip assay and data and bioinformatics analysis were carried out by Capitalbio Corporation (Beijing, China).

Techniques: Quantitative RT-PCR, Expressing, Comparison, Microarray

Journal: Scientific Reports

Article Title: Circular RNAs expression profiles in human gastric cancer

doi: 10.1038/s41598-017-09076-6

Figure Lengend Snippet: The numbers of potential targeted miRNAs of the differentially expressed circRNAs.

Article Snippet: The circRNAs expression profile microarray chip assay and data and bioinformatics analysis were carried out by Capitalbio Corporation (Beijing, China).

Techniques:

Journal: Scientific Reports

Article Title: Circular RNAs expression profiles in human gastric cancer

doi: 10.1038/s41598-017-09076-6

Figure Lengend Snippet: Represent circRNA-miRNA network. This network was based on the expression profile results and the related software. The 3 dysregulated circRNAs, hsa_circ_0076304, hsa_circ_0035431, and hsa_circ_0076305 (purple red nodes) having the highest magnitude of change, were predicted to be functionally connected with their targeted miRNAs in the network.

Article Snippet: The circRNAs expression profile microarray chip assay and data and bioinformatics analysis were carried out by Capitalbio Corporation (Beijing, China).

Techniques: Expressing, Software