Summary Report for Lung AWG Workshop 2 May 2011
Overview
Introduction

This is the summary report for run Lung AWG Workshop 2 May 2011 (lung_awg_workshop_2011_05_02__).

Summary

A total of 22 reports are available for run Lung AWG Workshop 2 May 2011 (lung_awg_workshop_2011_05_02__). No reports were found for the following Individual Sets:

Results
LUAD/00 [11]
Clinical Data Preprocess

View Report | 0 significant results

Clinical data for tier 1 clinical variables are generated.

Gistic2 Copy Number Analysis

View Report | 0 significant results

With data describing chromosomal aberrations in large tumor sets, the aberrations that drive tumorigenesis and the oncogenes and TSGs they most likely target can be identified if the following 4 issues are addressed: (i) The aberrations in each of the tumors must be accurately mapped; (ii) Driver aberrations that rise above the background rate of random passenger aberrations must be identified; (iii) For each driver aberration, the loci most likely to contain the targeted oncogenes or TSGs must be identified; (iv) Tumors must be classified as to whether they are aberrant at the predicted driver loci, so that the effects of those aberrations can be studied. The GISTIC algorithm tackles each issue in individual stages as discussed in [] and [].

Correlation between mRNA expression and clinical

View Report | 2 significant results

Testing the association between 17814 genes and 4 clinical features across 25 samples, statistically thresholded by P value <= 0.05 and Q value <= 0.25

Correlation between molecular cancer subtypes to clinical

View Report | 0 significant results

Testing the association between 2 clustering variables and 5 clinical features across 25 samples, no significant finding detected with P value <= 0.05 and Q value <= 0.25.

Correlation between gene mutation status and clinical

View Report | 0 significant results

Testing the association between mutation status of 27 genes and 6 clinical features across 44 samples, no significant finding detected with P value <= 0.05 and Q value <= 0.25.

Correlations between copy number and mRNA expression

View Report | 0 significant results

This page contains the calculated correlation coefficients based on measurements of genomic copy number (log2) values and intensitiy of the expressions of the the corresponding feature across patients. High positive/low negative correlation coefficients indicate that genomic alterations result in differences in the expressions of the features (microRNA or mRAN) the genomic regions transcribe.

Detected event calls for genes

View Report | 0 significant results

This page contains the detected genomic event calls for each gene. Genes marked with a genomic event are observed have the event occurs accross samples with a frequency over a set of thresholds. Number of genes that are mutated, amplified, and deleted are 18865, 216, and 687 respectively

Correlate Expression with Methylation

View Report | 0 significant results

The top 25 and bottom 25 methylation probe/gene pairs are displayed.

CNMF clustering of mRNA expression

View Report | 0 significant results

Using the median data set, we filtered the data to 1500 most variable genes. Consensus NMF clustering of 33 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Consensus hierarchical clustering of mRNA expression

View Report | 0 significant results

Using the median data set, we filtered the data to 1500 most variable genes. Consensus average linkage hierarchical clustering of 33 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Associate mutation, copy number alteration, and cancer subtype markers with pathways

View Report | 20 significant results

There are 5 pathways significantly enriched with genes with copy number gain/loss or mutation.

LUSC/00 [11]
Clinical Data Preprocess

View Report | 0 significant results

Clinical data for tier 1 clinical variables are generated.

Gistic2 Copy Number Analysis

View Report | 0 significant results

With data describing chromosomal aberrations in large tumor sets, the aberrations that drive tumorigenesis and the oncogenes and TSGs they most likely target can be identified if the following 4 issues are addressed: (i) The aberrations in each of the tumors must be accurately mapped; (ii) Driver aberrations that rise above the background rate of random passenger aberrations must be identified; (iii) For each driver aberration, the loci most likely to contain the targeted oncogenes or TSGs must be identified; (iv) Tumors must be classified as to whether they are aberrant at the predicted driver loci, so that the effects of those aberrations can be studied. The GISTIC algorithm tackles each issue in individual stages as discussed in [] and [].

Correlation between mRNA expression and clinical

View Report | 3 significant results

Testing the association between 17931 genes and one clinical feature across 59 samples, statistically thresholded by P value <= 0.05 and Q value <= 0.25

Correlation between molecular cancer subtypes to clinical

View Report | 0 significant results

Testing the association between 2 clustering variables and 5 clinical features across 59 samples, no significant finding detected with P value <= 0.05 and Q value <= 0.25.

Correlation between gene mutation status and clinical

View Report | 0 significant results

Testing the association between mutation status of 73 genes and 5 clinical features across 63 samples, no significant finding detected with P value <= 0.05 and Q value <= 0.25.

Correlations between copy number and mRNA expression

View Report | 0 significant results

This page contains the calculated correlation coefficients based on measurements of genomic copy number (log2) values and intensitiy of the expressions of the the corresponding feature across patients. High positive/low negative correlation coefficients indicate that genomic alterations result in differences in the expressions of the features (microRNA or mRAN) the genomic regions transcribe.

Detected event calls for genes

View Report | 0 significant results

This page contains the detected genomic event calls for each gene. Genes marked with a genomic event are observed have the event occurs accross samples with a frequency over a set of thresholds. Number of genes that are mutated, amplified, and deleted are 18865, 3920, and 5085 respectively

Correlate Expression with Methylation

View Report | 0 significant results

The top 25 and bottom 25 methylation probe/gene pairs are displayed.

CNMF clustering of mRNA expression

View Report | 0 significant results

Using the median data set, we filtered the data to 1500 most variable genes. Consensus NMF clustering of 134 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Consensus hierarchical clustering of mRNA expression

View Report | 0 significant results

Using the median data set, we filtered the data to 1500 most variable genes. Consensus average linkage hierarchical clustering of 134 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

Associate mutation, copy number alteration, and cancer subtype markers with pathways

View Report | 20 significant results

There are 5 pathways significantly enriched with genes with copy number gain/loss or mutation.

Methods & Data
Input

  • Firehose Directory = /home/radon00/nils/nozzle_summaries/lung

  • Run Prefix = lung_awg_workshop_2011_05_02__

  • Summary Report Date = Sun May 1 23:27:44 2011