Abstract:
:After the completion of sequencing for dozens of genomes, as well as the draft of human genome, a major challenge is to characterize genome-wide transcriptional regulation networks. Identification of regulatory functions for transcription factor binding sites in eukaryotes greatly enhances our understanding of the networks, as it has been done extensively under various physiological conditions in yeast. We propose a novel approach based on multivariate adaptive splines to modelling regulatory roles of motifs in gene expression time series data. By applying the proposed approach on two meiotic datasets, we identified well-documented motifs as well as some novel putative motifs that are involved in the transcriptome reprogramming. In addition to identifying single regulatory motifs, we also modelled and unravelled motifs that manifest their effects through coupling with others in regulatory networks. Our findings reveal the potential of multivariate adaptive splines in deciphering complex and important transcriptional regulatory networks in eukaryotes.
journal_name
Cancer Genomics Proteomicsjournal_title
Cancer genomics & proteomicsauthors
Chen X,Zhang Hsubject
Has Abstractpub_date
2008-01-01 00:00:00pages
55-62issue
1eissn
1109-6535issn
1790-6245journal_volume
5pub_type
杂志文章abstract:BACKGROUND:miRNAs play important roles in multiple biological processes, and deregulation has been linked to several human diseases, including cancer. Studying changes in miRNA expression in cancer development is commonly performed in vitro in human cancer cell lines using quantitative polymerase chain reaction (qPCR),...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2016-01-01 00:00:00
abstract::Cellular signal transduction pathways and gene expression are tightly regulated to accommodate changes in response to physiological environments. In the current study, molecules were identified that are activated as a result of intracellular signaling and immediately expressed as mRNA in MCF-7 breast cancer cells shor...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2008-05-01 00:00:00
abstract::Functional genomics has been applied in the study of human malignancies since the inception of this field nearly a decade ago. Microarray analysis has been specifically used in an attempt to re-classify carcinomas at the molecular level, to aid in diagnosis/prognosis and to predict how various types of tumour respond ...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2007-07-01 00:00:00
abstract::Breast cancer metastasis accounts for the majority of deaths from breast cancer. Detection of breast cancer metastasis at the earliest stage is important for the management and prediction of breast cancer progression. Emerging techniques using the analysis of circulating tumor cells show promising results in predictin...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章,评审
doi:
更新日期:2012-09-01 00:00:00
abstract:BACKGROUND:Oncogenic infection by HPV, eventually leads to cervical carcinogenesis, associated by deregulation of specific pathways and protein expression at the intracellular and secretome level. Thus, secretome analysis can elucidate the biological mechanisms contributing to cervical cancer. In the present study we s...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章,评审
doi:10.21873/cgp.20060
更新日期:2017-11-01 00:00:00
abstract::We present possible applications of Atomic Force Microscopy (AFM) as a force spectroscopy tool in genomics and proteomics. AFM applications in these fields have opened new opportunities for studying the mechanical properties of biomolecules and their interactions in their native environment, as well as in determining ...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章,评审
doi:
更新日期:2004-01-01 00:00:00
abstract:BACKGROUND:Metastasis associated gene-1 (MTA1), was initially discovered in aggressive human cancer cell lines and has been subsequently associated with the invasiveness and metastatic potential of cancer cells. MATERIALS AND METHODS:In the present study, we evaluated the expression levels of MTA1 in a cohort of human...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2015-05-01 00:00:00
abstract:BACKGROUND:Malignant pilomatricoma (MP) is a rare cancer of the hair matrix with only a few cases reported in literature. Given the rarity of this cancer and the lack of relevant genetic data, very little is known about the nature of the molecular pathophysiology except the involvement of the Catenin Beta 1 (CTNNB1)/Wn...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20233
更新日期:2020-11-01 00:00:00
abstract:BACKGROUND/AIM:The outcome of patients with advanced hepatocellular carcinoma (HCC) remains poor and therapeutic options, including sorafenib, the first anti-cancer drug proved to prolong survival in patients with advanced HCC, are limited. However, no clinically useful predictive biomarker for sorafenib has been repor...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20159
更新日期:2019-11-01 00:00:00
abstract:BACKGROUND:Pancreatic cancer, has a very high mortality rate and requires novel molecular targets for diagnosis and therapy. Genetic association studies over databases offer an attractive starting point for gene discovery. MATERIALS AND METHODS:The National Center for Biotechnology Information (NCBI) Phenome Genome In...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:The progression of colorectal cancer (CRC) mainly stems from the occurrence of somatic mutation. However, there is little information that can be used to comprehensively analyse the importance of germline variants in CRC patients. PATIENTS AND METHODS:The candidate germline variants between tumor relapse an...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20189
更新日期:2020-05-01 00:00:00
abstract:BACKGROUND:Breast cancer metastasis is associated with the motility and invasiveness of breast cancer cells. In a previous study we reported the motility enhancement effect of keratinocyte growth factor (KGF) on breast cancer cells. This study established and characterized the influence of KGF on breast cancer cell mot...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2004-07-01 00:00:00
abstract:AIM:This pilot study assessed the association of BIM deletion polymorphism and BIM RNA isoform in patients with EGFR-positive non-small cell lung cancer (NSCLC). PATIENTS AND METHODS:The study included 33 patients with EGFR-positive NSCLC treated with gefitinib. BIM deletion polymorphism and BIM RNA isoform (EL/L/S/γ)...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20010
更新日期:2016-01-01 00:00:00
abstract:BACKGROUND/AIM:Deregulated activation of signaling through the RAS/RAF/mitogen-activated protein kinase/extracellular signal-regulated kinase (RAS/RAF/MEK/ERK) and signal transducer and activator of transcription (STAT) pathways is involved in numerous hematological malignancies, making it an attractive therapeutic tar...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20208
更新日期:2020-09-01 00:00:00
abstract:BACKGROUND/AIM:In breast cancer, initiation of carcinogenesis leads to epigenetic dysregulation, which can lead for example to the loss of the heterochromatin skeleton SUV39H1/H3K9me3/HP1 or the supposed secondary skeleton TIP60/P400/H4K12ac/BRD (2/4), which allows the maintenance of chromatin integrity and plasticity....
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20223
更新日期:2020-11-01 00:00:00
abstract:BACKGROUND/AIM:Pseudomyogenic hemangioendothelioma is a rare endothelial tumor. Previous genetic investigations have shown that the tumors carry either a SERPINE1-FOSB or an ACTB-FOSB fusion gene. The aim of the study was to identify FOSB fusions linked with pseudomyogenic hemangioendothelioma. MATERIALS AND METHODS:R...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20134
更新日期:2019-07-01 00:00:00
abstract::Patients with pancreatic ductal adenocarcinoma have a dismall prognosis because at the time of diagnosis, in the vast majority of patients the tumor has already disseminated to distant organs and the therapeutic benefit of approved agents such as gemcitabine is limited. Therefore, the identification and preclinical an...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章,评审
doi:10.21873/cgp.20149
更新日期:2019-11-01 00:00:00
abstract:AIM:To identify and study targets of microRNA biomarkers of glioblastoma survival across events (death and recurrence) and phases (life expectancy or post-diagnostic) using functional and network analyses. MATERIALS AND METHODS:microRNAs associated with glioblastoma survival within and across race, gender, recurrence,...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2011-07-01 00:00:00
abstract:BACKGROUND:Inositol hexakisphosphate (IP6), a naturally occurring polyphosphorylated carbohydrate, has been reported to have significant in vivo and in vitro anticancer activity against numerous tumors. However, the molecular mechanism of the anticancer effect of IP6 has not been fully elucidated. MATERIALS AND METHOD...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Cigarette smoke (CS) is the main inducer of oral cancer, increasing its prevalence by 4-7 times. MATERIALS AND METHODS:We examined the suitability of cell models SCC-25 and SCC-15 for studying effects of CS on oral cancer cells and whether CS significantly affects the cell cycle using fluorescence-activated...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2015-03-01 00:00:00
abstract:AIM:Alpha B-Crystallin (CRYAB) is purported to be a metastasis suppressor protein, and lack or lower CRYAB expression is a prognostic biomarker for several types of cancer, such as that of the prostate and head and neck. However, the association of genomic variation of CRYAB and breast cancer is not well studied. The a...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2011-09-01 00:00:00
abstract:BACKGROUND/AIM:Medulloblastoma (MBL), an archetypal primitive neuroectodermal tumor of the cerebellum, is the most common pediatric central nervous system malignancy representing approximately 20% of all childhood brain tumors. Herein, we report on a new xenotransplantable tumor cell line, derived from a 6-year-old fem...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20037
更新日期:2017-07-01 00:00:00
abstract:BACKGROUND/AIM:Prostate cancer is the most common malignancy in US males. African American men have higher incidence and mortality rates than European Americans. Five single nucleotide polymorphisms are associated with PCa. We hypothesized haplotypes inferred from these SNPs are also associated with PCa. PATIENTS AND ...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20076
更新日期:2018-05-01 00:00:00
abstract::Tumorigenesis of glioblastoma multiforme (GBM), the most aggressive primary intracranial neoplasm, is associated with aberrant PI3K/AKT/mTOR signaling. Inhibitors of mTOR, such as rapamycin (RAPA) or its analogs, have provided limited benefit. Here, we aim to decipher the signaling pathways involved in RAPA resistance...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2009-09-01 00:00:00
abstract:BACKGROUND:Few studies have analyzed the association between human telomerase reverse transcriptase (hTERT) protein expression (nuclear and cytoplasmic localization), hTERT methylation status, and human papillomavirus (HPV) genotype infection in cervical cancer. PATIENTS AND METHODS:One hundred seventy-three patients ...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20218
更新日期:2020-09-01 00:00:00
abstract::Lung cancer is the leading cause of cancer-related to death in both men and women. Protein biomarkers for lung cancer were investigated using the expression of proteins from lung cancer cell line (A549) and compared with those of normal lung fibroblast cell line (MRC-5). Two-dimensional gel electrophoresis of A549 and...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2009-07-01 00:00:00
abstract:BACKGROUND:Trastuzumab is a monoclonal antibody against HER2-positive breast cancer. Despite improving the natural history of the disease, there is a number of patients who are resistant to it, whereas all patients will eventually develop resistance and disease will progress. Inconsistent preclinical data show that the...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20105
更新日期:2018-11-01 00:00:00
abstract::The expression profiles of the erythropoietin producing hepatocellular carcinoma (Eph) receptor family of tyrosine kinases have been previously shown to provide molecular signatures of normal breast cells, breast tumor cells and invasive breast carcinoma cells. In particular, the expression of EphB6 receptor is lost i...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2010-09-01 00:00:00
abstract:BACKGROUND:Salivary gland cancer is a common type of head and neck cancer characterized by occasional deep invasion and lung metastasis. The precise role of sex steroid hormones in salivary gland cancer is unclear. To address this issue, we investigated whether the estrogen axis modulates salivary adenocarcinoma (SAC) ...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:
更新日期:2016-07-01 00:00:00
abstract:BACKGROUND/AIM:Pul-down assay is a popular in vitro method for identification of physical interactors of selected proteins. Here, for the first time, we compared three conventional variants of pull-down assay with the streptavidin-modified surface plasmon resonance (SPR) chips for the detection of PDZ and LIM domain pr...
journal_title:Cancer genomics & proteomics
pub_type: 杂志文章
doi:10.21873/cgp.20098
更新日期:2018-09-01 00:00:00