Identification of the Ischemic Pathway Level Changes by Integrating Temporal Phosphoproteome in Ovarian Cancer

Date

2017-09-08

Author

Budak, Gungor
Fraenkel, Ernest
Tunçbağ, Nurcan

Metadata

Show full item record

Item Usage Stats

117
views

0
downloads

The temporal proteome studies aim to evaluate changes in the proteome and phosphoproteome when there is a delay in freezing tissues following tumor excision. Cold ischemia corresponds to the delay time to freezing post-excision. Recently, Carr and his colleagues have shown that ischemia does not affect the global proteome, but the phosphoproteome shows 10% change during ischemia. In this work, we use this published phosphoproteomic dataset derived from tumors of four ovarian cancer patients where the samples are frozen without any delay and with a delay of 5, 30 and 60 minutes [1]. We first analyzed the post-excision phosphorylation changes across different patients and showed that the ischemic effect is very heterogeneous at phosphoproteomic level. Then, we reconstructed patient-specific network models by inferring the confidence weighted interactome and phosphoproteome. For this purpose, we use the Omics Integrator software which solves the prize-collecting Steiner forest (PCSF) problem [2]. On the one hand, it tries to include as many of the proteomic hits as possible; on the other hand, it tries to keep the network small by avoiding using unreliable protein-protein interactions. Using these networks we are able to track enriched biological processes across time points. For example, many biological processes are significantly enriched in any tumors; i.e. apoptosis, cellular response to stress. We are also able to extract the biological processes that are significantly enriched at any time point and in any tumor. Next, we aligned the reconstructed patient-specific networks and identified common and unique pathways across these patients as well as important subnetworks. We also compared these networks based on the functional enrichments to identify the biological processes and pathways that play role in different patients. The results of this study provide us information about the ischemic pathways and proteins besides the cancer related pathways. Because in many studies including TCGA the excision time is not known, the benchmark ischemic pathways and proteins will make us be able to distinguish cancer-related pathways and ischemic artefacts.

Subject Keywords

Ischemia, Network Modeling, Omic Data Integration

URI

http://molbioturk.org/molbiyokon17/img/abstract_book.pdf
https://hdl.handle.net/11511/84430

Conference Name

5th International Congress ofthe Molecular Biology Association of Turkey (8 - 10 Eylül 2017)

Collections

Graduate School of Informatics, Conference / Seminar

Suggestions

OpenMETU
Core

Examination of the dielectrophoretic spectra of MCF7 breast cancer cells and leukocytes Çağlayan, Zeynep; Demircan Yalçın, Yağmur; Külah, Haluk (Wiley, 2020-03-01) The detection of circulating tumor cells (CTCs) in blood is crucial to assess metastatic progression and to guide therapy. Dielectrophoresis (DEP) is a powerful cell surface marker-free method that allows intrinsic dielectric properties of suspended cells to be exploited for CTC enrichment/isolation from blood. Design of a successful DEP-based CTC enrichment/isolation system requires that the DEP response of the targeted particles should accurately be known. This paper presents a DEP spectrum method to inve...
Determining the origin of synchronous multifocal bladder cancer by exome sequencing Acar, Omer; Ozkurt, Ezgi; Demir, Gulfem; Sarac, Hilal; ALKAN, CAN; Esen, Tarik; Somel, Mehmet; LACK, NATHAN (2015-11-09) Background: Synchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration (clonal) or spontaneous transformation of multiple cells by carcinogens (field effect). It is unclear which model is correct, with several studies supporting both hypotheses. A potential cause of this uncertainty may be the small number of genetic mutations previously used to quantify the relat...
IDENTIFICATION AND CHARACTERIZATION OF AN INTRONIC TRANSCRIPT FOR IGFBP4 Yılmaz, Utku Cem; Erson Bensan, Ayşe Elif; Department of Molecular Biology and Genetics (2023-1-20) Alternative polyadenylation is a widespread mRNA processing event affecting the length of the 3’UTR of mRNAs. Alternative use of polyadenylation sites sometimes occurs in terminal exons, proximal exons, or proximal introns, affecting the coding 3’UTR length and even the coding sequence of the mRNA. To identify estrogen (E2) related polyadenylation changes by a 3’-seq experiment, we detected an early intronic polyadenylation site for IGFBP4 (insulin-like growth factor binding protein 4). In this thesis, I pr...
Extraction of auditory evoked potentials from ongoing eeg Aydın, Serap; Gençer, Nevzat Güneri; Department of Electrical and Electronics Engineering (2005) In estimating auditory Evoked Potentials (EPs) from ongoing EEG the number of sweeps should be reduced to decrease the experimental time and to increase the reliability of diagnosis. The rst goal of this study is to demon- strate the use of basic estimation techniques in extracting auditory EPs (AEPs) from small number of sweeps relative to ensemble averaging (EA). For this purpose, three groups of basic estimation techniques are compared to the traditional EA with respect to the signal-to-noise ratio(SNR) ...
Diagnosis of malignant pleural mesothelioma from pleural fluid by Fourier transform-infrared spectroscopy coupled with chemometrics Abbas, Sherif; Ozek, Nihal Simsek; Emri, Salih; KÖKSAL, DENİZ; Severcan, Mete; Severcan, Feride (2018-10-01) This study was conducted to differentiate malignant pleural mesothelioma (MPM) from lung cancer (LC) and benign pleural effusion (BPE) from pleural fluids using the diagnostic power of Fourier transform-infrared spectroscopy with attenuated total reflectance mode coupled with chemometrics. Infrared spectra of MPM (n = 24), LC (n = 20), and BPE (n = 25) were collected, and hierarchical cluster analysis (HCA) and principal component analysis (PCA) were applied to their spectra. HCA results indicated that MPM ...

Citation Formats

G. Budak, E. Fraenkel, and N. Tunçbağ, “Identification of the Ischemic Pathway Level Changes by Integrating Temporal Phosphoproteome in Ovarian Cancer,” presented at the 5th International Congress ofthe Molecular Biology Association of Turkey (8 - 10 Eylül 2017), İstanbul, Türkiye, 2017, Accessed: 00, 2021. [Online]. Available: http://molbioturk.org/molbiyokon17/img/abstract_book.pdf.