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Identification of aberrant pathways and network activities from high-throughput data

J. Wang, Y. Zhang, C. Marian, H. W. Ressom
2012 Briefings in Bioinformatics  
This review presents recent progress in using high-throughput biological assays to decipher aberrant pathways and network activities.  ...  In particular, this review provides specific examples in which high-throughput data have been applied to identify relationships between diseases and aberrant pathways and network activities.  ...  We appreciate the organizers and participants of the Workshop on Identification of Aberrant Pathway and Network Activity from High-Throughput Data at the 2011 Pacific Biocomputing Symposium for providing  ... 
doi:10.1093/bib/bbs001 pmid:22287794 pmcid:PMC3404398 fatcat:woielqwwtbc6bhdoub3hycnu6a

"Lineage Addiction" in Human Cancer: Lessons from Integrated Genomics

L.A. GARRAWAY, B.A. WEIR, X. ZHAO, H. WIDLUND, R. BEROUKHIM, A. BERGER, D. RIMM, M.A. RUBIN, D.E. FISHER, M.L. MEYERSON, W.R. SELLERS
2005 Cold Spring Harbor Symposia on Quantitative Biology  
learning algorithms in common use.  ...  Moreover, analysis of the signal intensities that result from genomic DNA hybridization, and comparison to corresponding signal data from normal genomes, allow determination of copy number changes present  ... 
doi:10.1101/sqb.2005.70.016 pmid:16869735 fatcat:7f2ithdlurcedigm6ckns4urbe

Oral Presentations

2003 Analytical Cellular Pathology  
The increased insights into molecular pathways, gained from high throughput 'functional genomics', using DNA-and protein-chip approaches and specially-designed animal model systems, will open great perspective  ...  O.47 HIGH THROUGHPUT LOSS-OF-FUNCTION PHENOTYPIC SCREENS IN MAMMALIAN CELLS USING RNA INTERFERENCE R.  ... 
doi:10.1155/2003/473736 fatcat:amhylvhuabbclccos4xwvxqhmq

A growing family: Adding mutated Erbb4 as a novel cancer target

Udo Rudloff, Yardena Samuels
2010 Cell Cycle  
Erbbs are receptor tyrosine kinases that are important regulators of several signaling pathways.  ...  Functional analysis of seven of its mutations was shown to increase its catalytic and transformation abilities as well as providing essential survival signals.  ...  Downstream targets The most commonly affected signaling pathways by aberrant Erb signal transduction are the PI3K-Akt and MAP kinase pathways.  ... 
doi:10.4161/cc.9.8.11239 pmid:20404484 pmcid:PMC3384517 fatcat:fx3bmfkadrbabortxbxgpl4x34

Global Protein-expression Analysis of Bone and Soft Tissue Sarcomas

Akira Kawai, Tadashi Kondo, Yoshiyuki Suehara, Kazutaka Kikuta, Setsuo Hirohashi
2008 Clinical Orthopaedics and Related Research  
Proteomic analysis using 2D-DIGE provides novel information on the biology of bone and soft tissue sarcomas that could be used to diagnosis and treat these tumors.  ...  Using two-dimensional difference gel electrophoresis (2D-DIGE) and mass spectrometry, we performed global protein expression studies of bone and soft tissue sarcomas to develop novel diagnostic and therapeutic  ...  These genetic alterations initiate changes in a series of signal transduction pathways and develop malignant tumor cells.  ... 
doi:10.1007/s11999-008-0330-4 pmid:18535868 pmcid:PMC2493021 fatcat:fzue2npcabhetkhaugkmlkinjq

Global transcriptome and sequenome analysis of formalin-fixed salivary epithelial-myoepithelial carcinoma specimens

Isabel Fonseca, Achim Bell, Khalida Wani, Diana Bell
2014 Genes, Chromosomes and Cancer  
The transcripts were annotated using NCBI Entrez Gene, and computationally analyzed with the Ingenuity Pathway Analysis program.  ...  Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using a whole-transcriptome shotgun sequencing experiment.  ...  Pathway Analysis The extracellular matrix (ECM) pathway network was created using the Ingenuity Pathway Analysis (IPA) program from Ingenuity Systems (http://www.ingenuity.com/).  ... 
doi:10.1002/gcc.22238 pmid:25546727 pmcid:PMC4845898 fatcat:dlalsdwibvgito2zgd7cpbkzwu

Clinical proteomics: present and future prospects

Nicole M Verrills
2006 Clinical biochemist reviews  
This review summarises the advances in proteomics that has propelled us to this exciting age of clinical proteomics, and highlights the future work that is required for this to become a reality.  ...  A number of technical obstacles remain before routine proteomic analysis can be achieved in the clinic; however the standardisation of methodologies and dissemination of proteomic data into publicly available  ...  Importantly, the development of specialised software algorithms that rapidly search MS data against known or predicted proteins within databases makes this process amenable to high throughput analysis.  ... 
pmid:17077880 pmcid:PMC1579414 fatcat:o3jxldrmafafbec6w6slc6tx4u

Challenges in cancer research and multifaceted approaches for cancer biomarker quest

Jirina Martinkova, Suresh Jivan Gadher, Marian Hajduch, Hana Kovarova
2009 FEBS Letters  
Currently, a wide range of proteomic technologies are being used in quest for new cancer biomarkers with effective use.  ...  Despite better insight into genomic aberrations and diversity of cancer phenotypes, it is apparent that proteomics too deserves attention in cancer research.  ...  Acknowledgements We acknowledge support of grants from the Czech Ministry of School and Education (MSM6198959216 and LC07017) and Institutional Research Concept AV0Z50450515.  ... 
doi:10.1016/j.febslet.2009.03.042 pmid:19327356 fatcat:ai5dhhjafjfv5kqnvu7gfbb4qy

Pre-clinical validation of an RNA-based precision oncology platform for patient-therapy alignment in a diverse set of human malignancies resistant to standard treatments [article]

Prabhjot S. Mundi, Filemon S. Dela Cruz, Adina Grunn, Daniel Diolaiti, Audrey Mauguen, Armaan Siddiquee, Daoqi You, Ron Realubit, Charles Karan, Michael V. Ortiz, Melissa Accordino, Zvika Aloni (+39 others)
2021 bioRxiv   pre-print
Joint analysis of tumors—from patients with distinct malignancies who had progressed on multiple lines of therapy—and drug perturbation transcriptional profiles predicted sensitivity to 28 of 350 drugs  ...  Drugs were prioritized based on their ability to either invert the activity of individual Master Regulator proteins, with available high-affinity inhibitors, or of the modules they comprise (Tumor-Checkpoints  ...  Automated high-throughput screens were performed in all cell lines using the PLATESeq platform. Table S4 .  ... 
doi:10.1101/2021.10.03.462951 fatcat:fcxdpopqjndm7cr5suhrjsfiyi

A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics

I. Baianu
2012 Nature Precedings  
of cancer signaling pathways and epigenetic mechanisms.  ...  Multiple sample analyses from several recent clinical studies have shown that gene expression data for cancer cells can be employed to distinguish between tumor types as well as to predict outcomes.  ...  Acknowledgements The author gratefully acknowledges receiving helpful suggestions, pertinent documentation and critical comments from: Dr.  ... 
doi:10.1038/npre.2012.7052.1 fatcat:2i2iaewtzjbizmlxbbg5zpporq

Clinical Trials in Cancer and Pharmacogenomics: A Critical Evaluation

I.C. Baianu
2012 Journal of Clinical Trials  
of cancer signaling pathways and epigenetic mechanisms.  ...  A critical overview of recent clinical trials in cancer is presently focused on signaling pathway blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer  ...  Acknowledgements The author gratefully acknowledges receiving helpful suggestions, pertinent documentation and critical comments from: Dr.  ... 
doi:10.4172/2167-0870.1000109 fatcat:jckilr6dzjgynhnvjdvbsni6pe

SYSTEMIC MASTOCYTOSIS: MOLECULAR LANDSCAPE AND IMPLICATIONS FOR TREATMENT

Cecilia Monaldi, Sara De Santis, Manuela Mancini, Samantha Bruno, Michele Cavo, Simona Soverini
2021 Mediterranean Journal of Hematology and Infectious Diseases  
The interaction between KIT and its ligand leads to dimerization of the receptor and activation of its intrinsic tyrosine kinase activity and drives a variety of downstream signal transduction pathways  ...  SETD2 loss of function in acute leukemias is often associated with chromosomal aberrations and activated gene expression in the mTOR and Jak/Stat signaling pathways, contributing directly to leukemogenesis  ... 
doi:10.4084/mjhid.2021.046 fatcat:asmenuew7nbabed5mh2ysujlce

Complex Systems Analysis of Cell Cycling Models in Carcinogenesis

I. Baianu
2011 Nature Precedings  
One such family of pathways contains the cell cyclins.  ...  This novel theoretical analysis based on recently published studies of cyclin signaling, with special emphasis placed on the roles of cyclins D1 and E, suggests novel clinical trials and rational therapies  ...  The vast amounts of data becoming available from such high throughput measurements with microarrays on human tumors and tissues also require the employment of powerful computers, effective algorithms for  ... 
doi:10.1038/npre.2011.6205.1 fatcat:adtbpz5ccrbejh6gqarudwz5u4

Poster Presentations May 4–7, 2008

2008 Cellular Oncology  
Conclusions: Our preliminar data suggest, that gene expression was modified during tumuor transformation, and that this molecular changing system was reproducible.  ...  Statistical analysis were also performed intra and inter patients group using a GeneSpring software GX.3.  ...  Novel candidate loci include genes coding for proteins with important functions in the extracellular matrix, angiogenesis and cell migration, enzymes involved in the regulation of signal-transduction pathways  ... 
doi:10.1155/2008/925763 doaj:8f1677eb0d3241eebf136c5287538644 fatcat:2vrtdvxi5nc5zfnkhtf3dget6a

Identification of Wee1 as target in combination with avapritinib for Gastrointestinal Stromal Tumor treatment

Shuai Ye, Dinara Sharipova, Marya Kozinova, Lillian R Klug, Jimson W D'Souza, Martin G Belinsky, Katherine J Johnson, Margret B Einarson, Karthik Devarajan, Yan Zhou, Samuel Litwin, Michael C Heinrich (+4 others)
2020 JCI Insight  
Using Multiplexed Inhibitor Beads and Mass Spectrometry, we explored the majority of the kinome in GIST specimens from the three most common molecular subtypes (KIT-mutant, PDGFRA-mutant, Succinate dehydrogenase  ...  These studies provide strong preclinical justification for the use of MK-1775 in GIST.  ...  We acknowledge the following facilities at FCCC for their work contributing to this manuscript: Biosample Repository, Cell Sorting, High Throughput Screening, Genotyping and Real-Time PCR, and the Laboratory  ... 
doi:10.1172/jci.insight.143474 pmid:33320833 pmcid:PMC7934848 fatcat:nx4diaq3mzfqhl4w52zsnkdjuu
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