Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles

Edelman, Elena J.; Porrello, Alessandro; Guinney, Justin; Balakumaran, Bala S.; Bild, Andrea; Febbo, Phillip G.; Mukherjee, Sayan

doi:10.1093/bioinformatics/btl231

Cited by 63 publications

(61 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These genes were compared with the genes included in other prognostic lung cancer signatures, such as Beer et al Biology of ES in lung adenocarcinoma. To deepen our investigation of the biological underpinnings of the ES phenotype, we applied previously validated approaches, including Gene Set Enrichment Analysis (21,22) and Analysis of Sample Set Enrichment Scores (19,20), to cell lines that constitute our 100-gene lung cancer-specific classifier. Elucidation of patterns of pathway activation specific to ES in lung adenocarcinoma revealed numerous biologically relevant features (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Lung adenocarcinomas that share a common gene expression pattern with normal embryonic stem cells were associated with decreased survival, increased activation of oncogenic pathways, and increased likelihood of resistance to cisplatin, indicating the aggressiveness of these tumors. set enrichment for each sample in a gene expression data set (19,20). It expands on Gene Set Enrichment Analysis 9 (version 2.0), which is an analytic tool for relating gene expression data to gene sets to identify unifying biological themes (21,22).…”

Section: Translational Relevancementioning

confidence: 99%

See 1 more Smart Citation

Characterizing the Clinical Relevance of an Embryonic Stem Cell Phenotype in Lung Adenocarcinoma

Stevenson¹,

Mostertz²,

Acharya³

et al. 2009

Clinical Cancer Research

View full text Add to dashboard Cite

Purpose: Cancer cells possess traits reminiscent of those ascribed to normal stem cells.It is unclear whether these phenotypic similarities are the result of a common biological phenotype, such as regulatory pathways. Experimental Design: Lung cancer cell lines with corresponding gene expression data and genes associated with an embryonic stem cell identity were used to develop a signature of embryonic stemness (ES) activity specific to lung adenocarcinoma. Biological characteristics were elucidated as a function of cancer biology/oncogenic pathway dysregulation. The ES signature was applied to three independent early-stage (I-IIIa) lung adenocarcinoma data sets with clinically annotated gene expression data. The relationship between the ES phenotype and cisplatin (current standard of care) sensitivity was evaluated. Results: Pathway analysis identified specific regulatory networks [Ras (P = 0.0005), Myc (P = 0.0224), wound healing (P < 0.0001), chromosomal instability (P < 0.0001), and invasiveness (P < 0.0001)] associated with the ES phenotype. The prognostic relevance of the ES signature, as related to patient survival, was characterized in three cohorts [CALGB 9761 (n = 82; P = 0.0001), National Cancer Institute Director's Challenge Consortium (n = 442; P = 0.0002), and Duke (n = 45; P = 0.06)]. The ES signature was not prognostic in prostate, breast, or ovarian adenocarcinomas. Lung tumors (n = 569) and adenocarcinoma cell lines (n = 31) expressing the ES phenotype were more likely to be resistant to cisplatin (P < 0.0001 and P = 0.006, respectively). Conclusions: Lung adenocarcinomas that share a common gene expression pattern with normal human embryonic stem cells were associated with decreased survival, increased biological complexity, and increased likelihood of resistance to cisplatin. This indicates the aggressiveness of these tumors. (Clin Cancer Res 2009;15(24):7553-61)

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Translational Relevancementioning

confidence: 99%

Characterizing the Clinical Relevance of an Embryonic Stem Cell Phenotype in Lung Adenocarcinoma

Stevenson¹,

Mostertz²,

Acharya³

et al. 2009

Clinical Cancer Research

View full text Add to dashboard Cite

show abstract

“…Expression profiles are displayed using Treeview (32). Classification and clustering for pathway level analysis were performed by using gene sets ASSESS (Analysis of Sample Set Enrichment Scores), available on line (33). ASSESS provides a measure of enrichment of each gene set in each sample.…”

Section: Mammosphere Formation and Facs Analysis Of Stem Cellmentioning

confidence: 99%

Cell Fate Determination Factor Dachshund Reprograms Breast Cancer Stem Cell Function

Jiao

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

“…GSEA was performed using GSEA 1.0 (http://www.broad.mit.edu/gsea/) (Subramanian et al, 2005). ASSESS (Edelman et al, 2006) was also employed.…”

Section: Dataset Analysismentioning

confidence: 99%

“…Using gene sets defined through various methods including experimental perturbations and literature-based studies, GSEA provides a pathway discovery tool. A variation on GSEA, termed ASSESS, allows a measure of enrichment of gene sets across multiple samples (Edelman et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Patterns of cell signaling pathway activation that characterize mammary development

et al. 2008

View full text Add to dashboard Cite

Previous work has detailed the histological and biochemical changes associated with mammary development and remodeling. We have now made use of gene expression profiling, and in particular of the previously described signatures of cell signaling pathway activation, to explore the events associated with mammary gland development. We find that there is elevated E2F-specific pathway activity prior to lactation and relatively low levels of other important signaling pathways, such as RAS, MYC and SRC. Upon lactation and continuing into the involution phase, these patterns reverse with a dramatic increase in RAS, SRC and MYC pathway activity and a decline in E2F activity. At the end of involution, these patterns return to that of the adult non-lactating mammary gland. The importance of the changes in E2F pathway activity, particularly during the proliferative phase of mammary development, was confirmed through the analysis of mice deficient for various E2F proteins. Taken together, these results reveal a complex pattern of pathway activity in relation to the various phases of mammary gland development.

show abstract

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles

Abstract: Versions are available in Octave and Java (with a graphical user interface). Software can be downloaded at http://people.genome.duke.edu/assess.

Cited by 63 publications

References 22 publications

Characterizing the Clinical Relevance of an Embryonic Stem Cell Phenotype in Lung Adenocarcinoma

Characterizing the Clinical Relevance of an Embryonic Stem Cell Phenotype in Lung Adenocarcinoma

Cell Fate Determination Factor Dachshund Reprograms Breast Cancer Stem Cell Function

Patterns of cell signaling pathway activation that characterize mammary development

Contact Info

Product

Resources

About