Journal ArticleDOI
Large-scale integration of microarray data reveals genes and pathways common to multiple cancer types.
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TLDR
The results point to the value of integrating microarray data in the study of combination drug therapies targeting metastasis and the integrated significance analysis of microarrays approach produced top 400 gene lists for each of the 13 cancer types.Abstract:
The global gene expression analysis of cancer and healthy tissues typically results in large numbers of genes that are significantly altered in cancer. Such data, however, has been difficult to interpret due to the high level of variation of gene lists across laboratories and the small sample sizes used in individual studies. In this investigation, we compiled microarray data obtained from the same platform family from 84 laboratories, resulting in a database containing 1,043 healthy tissue samples and 4,900 cancer samples for 13 different tissue types. The primary cancers considered included adrenal gland, brain, breast, cervix, colon, kidney, liver, lung, ovary, pancreas, prostate and skin tissues. We normalized the data together and analyzed subsets for the discovery of genes involved in normal to cancer transformation. Our integrated significance analysis of microarrays approach produced top 400 gene lists for each of the 13 cancer types. These lists were highly statistically enriched with genes already associated with cancer in research publications excluding microarray studies (p < 1.31 E - 12). The genes MTIM and RRM2 appeared in nine and TOP2A in eight lists of significantly altered genes in cancer. In total, there were 132 genes present in at least four gene lists, 11 of which were not previously associated with cancer. The list contains 17 metal ions and 15 adenyl ribonucleotide binding proteins, six kinases and six transcription factors. Our results point to the value of integrating microarray data in the study of combination drug therapies targeting metastasis.read more
Citations
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Transcriptome reprogramming by cancer exosomes: identification of novel molecular targets in matrix and immune modulation.
Fatima Qadir,Mohammad Arshad Aziz,Chrisdina Puspita Sari,Hong Ma,Haiyan Dai,Xun Wang,Dhiresh Raithatha,Lucas Girotto Lagreca Da Silva,Muhammad Ali Hussain,Seyedeh P. Poorkasreiy,Iain Hutchison,Ahmad Waseem,Muy-Teck Teh,Muy-Teck Teh +13 more
TL;DR: Both normal and cancer exosomes modulated unique gene expression pathways in normal recipient cells, and molecular pathways and biomarkers identified may be clinically exploitable for developing novel liquid-biopsy based diagnostics and immunotherapies.
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Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis.
TL;DR: This study suggests that multiple and diverse respiratory viruses invoke several common host response pathways, and suggests five new therapeutic indications for existing small molecules or biological agents targeting proteins encoded by the genes F3, IL1B, TNF, CASP1 and MMP9.
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TOP2A is overexpressed and is a therapeutic target for adrenocortical carcinoma
TL;DR: The results suggest that TOP2A is overexpressed in ACC, regulates cellular proliferation and invasion in ACC cells, and is an attractive target for ACC therapy.
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Small extracellular vesicles in cancer.
TL;DR: Extracellular Vesicles (EV) are lipid-bilayer enclosed vesicles in submicron size that are released from cells to regulate initiation, growth, metastasis and invasion of tumors as mentioned in this paper.
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Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program
Douglas G. Walker,Alexis M. Whetzel,Geidy E. Serrano,Lucia I. Sue,Lih-Fen Lue,Thomas G. Beach +5 more
TL;DR: It is shown that high quality RNA can be produced from most human autopsy tissues, though with significant differences between tissues and donors, and did not depend solely on PMI.
References
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TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
Journal ArticleDOI
Significance analysis of microarrays applied to the ionizing radiation response
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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
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Journal ArticleDOI
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Rafael A. Irizarry,Bridget G. Hobbs,Francois Collin,Yasmin Beazer-Barclay,Kristen J. Antonellis,Uwe Scherf,Terence P. Speed +6 more
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Journal ArticleDOI
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Glynn Dennis,Brad T. Sherman,Douglas A. Hosack,Jun Jun Yang,Wei Gao,H. Clifford Lane,Richard A. Lempicki +6 more
TL;DR: DAMID is a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries that assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.
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