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Mining LINE-1 Characteristics That Mediate Gene Expression [chapter]

Naruemon Pratanwanich, Apiwat Mutirangura, Chatchawit Aporntewan
2010 Communications in Computer and Information Science  
We proposed to use data mining to identify LINE-1 (L1) characteristics that were associated with gene expression in bladder cancer. The data were collected from L1Base and GSE3167.  ...  All the significant rules were concentrated only in 20 characteristics. We were able to infer the L1 characteristics that down-regulated genes.  ...  Conclusion We have mined L1 characteristics that are associated with gene expression in bladder cancer.  ... 
doi:10.1007/978-3-642-16750-8_8 fatcat:tecpjzts5fdddnrjxdoaupg2ba

A Systems Biological Approach Reveals Multiple Crosstalk Mechanism between Gram-Positive and Negative Bacterial Infections: An Insight into Core Mechanism and Unique Molecular Signatures

Muthukumar. R, Alexandar. V, Berla Thangam, Shiek S. S. J. Ahmed, Markus M. Heimesaat
2014 PLoS ONE  
Further, to identify candidate molecules, the TLRs specific nodes were prioritized using microarray differential expressed genes. Of the top prioritized TLR 2 molecules, 70% were co-expressed.  ...  We used bioinformatics concepts, including literature mining to construct protein-protein interaction network, prioritization of TLRs specific nodes using microarray data and pathway analysis.  ...  Introduction Innate immune system is the first line of defense against invading pathogens that are highly conserved across species [1] .  ... 
doi:10.1371/journal.pone.0089993 pmid:24587173 pmcid:PMC3938579 fatcat:ptfvyowvqferjmtknyi7va6q7i

Identification of differentially expressed genes in breast cancer

Susana Salceda, Carrie Drumright, Anthony DiEgidio, Brandon Liang, Ping Hu, Yongming Sun, Vu Viet Hoang, Andrei Munteanu, Herve Recipon, Robert Cafferkey, Roberto A. Macina
2001 Nature Genetics  
Mining the cDNA database, we identified genes or expressed sequence tags (ESTs) that showed breast tissue specificity and upregulation in cancer.  ...  Compared with the expression levels in untreated cells, transcripts that were upregulated by both B[a]P and BPDE included members of the cytochrome P450, AP-1 (Fra-1, Fra-2) and glutathione S-transferase  ...  Mining the cDNA database, we identified genes or expressed sequence tags (ESTs) that showed breast tissue specificity and upregulation in cancer.  ... 
doi:10.1038/87276 fatcat:2resd2rxezakjnzecjqk6s3ske

MINE is a method for detecting spatial density of regulatory chromatin interactions based on a MultI-modal NEtwork [article]

Haiyan Gong, Minghong Li, Mengdie Ji, Xiaotong Zhang, Zan Yuan, Sichen Zhang, Yi Yang, Chun Li, Yang Chen
2022 bioRxiv   pre-print
Chromatin interactions play essential roles in chromatin conformation and gene expression. However, few tools exist to analyze the spatial density of regulatory chromatin interactions.  ...  Changes in SD-RCI before and after treating the HeLa cells with 1,6-hexanediol showed that the change in chromatin volume was related to the degree of activation or repression of genes in chromatin interactions  ...  This shows that the differential loops of MINE_enhanced_hic compared to Raw_hic are enriched for genes functionally related to characteristics of that cell line.  ... 
doi:10.1101/2022.07.11.499656 fatcat:p6t42r65dnh5rpg2elodfpj4o4

Page 1371 of None Vol. 42, Issue 2 [page]

2000 None  
With the use of transient expression in COS cells, it has been shown that EAAT1- and EAAT3-mediated .-glutamate uptake exhibit similar inhibition profiles and kinetic characteristics (1).  ...  Five different that could mediate g genes encoding five polypeptides lutamate uptake through an X, ¢ transport system have been cloned, and two of them, KAATI and EAATS, are expressed in peripheral or-  ... 

Integrating Clinical and Genomic Information Through the PrognoChip Mediator [chapter]

Anastasia Analyti, Haridimos Kondylakis, Dimitris Manakanatas, Manos Kalaitzakis, Dimitris Plexousakis, George Potamias
2006 Lecture Notes in Computer Science  
This is split into several query forms, allowing cancerous sample selection (along with their associated gene expression profiles and patient characteristics), based on criteria of interest.  ...  This requires not only an understanding of the genetic basis of the disease, based on the patient's tumor gene expression profiles but also the correlation of this data with knowledge normally processed  ...  Then, by the appropriate data-mining and gene-selection methods, find the genes that best discriminate between these two groups (i.e., disease-related gene markers). • By clustering the tumor gene expression  ... 
doi:10.1007/11946465_23 fatcat:xmfkzhvivre3jky7c46vdg25ua

STROBE-compliant integrin through focal adhesion involve in cancer stem cell and multidrug resistance of ovarian cancer

Luwei Wei, Fuqiang Yin, Wei Zhang, Li Li
2017 Medicine  
Pathway enrichment of CSC genes associated with drug resistance in ovarian cancer indicated that focal adhesion signaling might play important roles in CSC genes-mediated drug resistance.  ...  the Gene Expression Omnibus (GEO) Profiles.  ...  Table 1 Gene expression datasets related to chemotherapy response in ovarian CSCs retrieved from GEO Profiles.  ... 
doi:10.1097/md.0000000000006345 pmid:28328815 pmcid:PMC5371452 fatcat:sqakkh6havftlbr64zs2r6icrq

Knockdown of GTPBP4 inhibits cell growth and survival in human hepatocellular carcinoma and its prognostic significance

Wen-Bin Liu, Wei-Dong Jia, Jin-Liang Ma, Ge-Liang Xu, Hang-Cheng Zhou, Yan Peng, Wei Wang
2017 OncoTarget  
in HCC cell lines.  ...  Gene microarray and further pathway enrichment analyses indicated that ERBB signaling pathway was the most significantly changed one.  ...  The gene silencing efficiency mediated by lentivirus was further determined using qPCR after culturing for 5 days, and it was shown that in both cell lines, GTPBP4 expression at mRNA level was inhibited  ... 
doi:10.18632/oncotarget.21500 pmid:29212203 pmcid:PMC5706849 fatcat:h7j5wkuvgvfhllq4ywyuhjal5a

Epithelial-to-Mesenchymal Transition and Autophagy Induction in Breast Carcinoma Promote Escape from T-cell-Mediated Lysis

I. Akalay, B. Janji, M. Hasmim, M. Z. Noman, F. Andre, P. De Cremoux, P. Bertheau, C. Badoual, P. Vielh, A. K. Larsen, M. Sabbah, T. Z. Tan (+5 others)
2013 Cancer Research  
Our results argue that in addition to promoting invasion and metastasis EMT also profoundly alters the susceptibility of cancer cells to T-cell-mediated immune surveillance.  ...  This response was critical for susceptibility to CTL-mediated lysis because siRNA-mediated silencing of beclin1 to inhibit autophagy in target cells restored their susceptibility to CTL-induced lysis.  ...  Mien-Chie Hung at the MD Anderson Cancer Center for providing the MCF-7 (WT and SNAI1-6SA) cell lines. Grant Support  ... 
doi:10.1158/0008-5472.can-12-2432 pmid:23436798 fatcat:x4fo55beyvg6thzvyavecjr4ua

The c-myc Insulator Element and Matrix Attachment Regions Define the c-myc Chromosomal Domain

W. M. Gombert, S. D. Farris, E. D. Rubio, K. M. Morey-Rosler, W. H. Schubach, A. Krumm
2003 Molecular and Cellular Biology  
The enhancer-blocking activity is mediated by CTCF.  ...  This region harbors the c-myc insulator element (MINE), which contains at least two physically separable, functional activities: enhancerblocking activity and barrier activity.  ...  sensitivity to DNase I was identified as a characteristic feature that distinguishes the chromatin of transcribed and silent genes (46) .  ... 
doi:10.1128/mcb.23.24.9338-9348.2003 pmid:14645543 pmcid:PMC309672 fatcat:xxaddsogt5dvre53ngcmlmmz6e

Low BIN3 Expression is an Independent Predictor of Unfavorable Survival in Patients With Primary Colorectal Cancer

Jifang Cui, Yandi Liu, Heng Zhang, Yijia Wang, Guang Liu, Weihua Zhang, Chunze Zhang
2017 Technology in Cancer Research and Treatment  
Kyoto Encyclopedia of Genes and Genomes analysis indicated that the genes correlated with bridging integrator-3 (absolute Pearson r !  ...  Colorectal cancer cell lines, LoVo and HT29 cells, were used as in vitro cell model to assess the effect of demethylation on bridging integrator-3 expression.  ...  Results showed that the genes were enriched in sphingolipid signaling pathway, natural killer cell-mediated cytotoxicity, p53 signaling pathway, and apoptosis ( Figure 4 and Supplemental Table 2 ).  ... 
doi:10.1177/1533034617747774 pmcid:PMC5762098 fatcat:gqipqbnk7ragbpd2ls2nnabq3e

Ras-Mediated Deregulation of the Circadian Clock in Cancer

Angela Relógio, Philippe Thomas, Paula Medina-Pérez, Silke Reischl, Sander Bervoets, Ewa Gloc, Pamela Riemer, Shila Mang-Fatehi, Bert Maier, Reinhold Schäfer, Ulf Leser, Hanspeter Herzel (+3 others)
2014 PLoS Genetics  
-mediated transcription can generate the circadian phenotypes similar to those observed in metastatic cell lines.  ...  Using an inducible RAS expression system, we show that overexpression of RAS disrupts the circadian clock and leads to an increase of the circadian period while RAS inhibition causes a shortening of period  ...  (DOC)Text S3 Analysis of circadian expression data for the genes of interest indicates enrichment in circadian genes. Table 1 . 1 Circadian properties vary within the different cell lines.  ... 
doi:10.1371/journal.pgen.1004338 pmid:24875049 pmcid:PMC4038477 fatcat:dux3epi4ubdy7a7mdpvmacuh64

DNA Repair Pathway Gene Expression Score Correlates with Repair Proficiency and Tumor Sensitivity to Chemotherapy

S. P. Pitroda, I. M. Pashtan, H. L. Logan, B. Budke, T. E. Darga, R. R. Weichselbaum, P. P. Connell
2014 Science Translational Medicine  
The Recombination Proficiency Score (RPS) utilizes the expression levels for four genes involved in DNA repair pathway preference (RIF1, PARI, RAD51, and Ku80), such that high expression of these genes  ...  Carcinoma cells with low RPS exhibit HR suppression and frequent DNA copy number alterations, which are characteristic of error-prone repair processes that arise in HR-deficient backgrounds.  ...  To accomplish this, we developed a scoring system that correlates gene expression patterns with HR proficiency in human cancer cell lines.  ... 
doi:10.1126/scitranslmed.3008291 pmid:24670686 pmcid:PMC4889008 fatcat:dkczq7qttraetcewtvwyq7grs4

Identification of Novel Pretranslational Regulatory Mechanisms for NF-κB Activation

Xiao Huang, Ren Gong, Xinyuan Li, Anthony Virtue, Fan Yang, Irene H. Yang, Anh H. Tran, Xiao-Feng Yang, Hong Wang
2013 Journal of Biological Chemistry  
Thirty-eight NF-B-signaling genes are analyzed for tissue expression profile and pretranscriptional mechanisms.  ...  Results: NF-B-signaling genes are differentially expressed and can be regulated by specific transcription factors, multiple alternative promoters/spliced isoforms, DNA methylation, and microRNAs.  ...  This result suggests that C/EBPs may mediate the NF-B signal gene induced by IL-1␤ and TNF-␣ and that the NF-B signal gene mediates IL-1␤and TNF-␣-induced self-amplification of the NF-B pathway via a positive  ... 
doi:10.1074/jbc.m113.460626 pmid:23515310 pmcid:PMC3668723 fatcat:jgntiqs5ircpbdz7o65526s5ky

An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells

Seungyoon Nam, Xinghua Long, ChangHyuk Kwon, Sun Kim, Kenneth P Nephew
2012 BMC Genomics  
Conclusions: By integrating miRNA-related network, gene/miRNA expression and text-mining, the current study provides a computational-based systems biology approach for further investigating the molecular  ...  Previously, we derived two drug-resistant breast cancer sublines (tamoxifen-and fulvestrant-resistant cell lines) from the MCF7 breast cancer cell line and performed genome-wide mRNA and microRNA profiling  ...  In summary, cluster 1 shows that miR-146a and BRCA1/2 are shared molecular characteristics of the tamoxifen and the fulvestrant resistances (genomic stability fine-tuning, PI3KCA mutation) and are closely  ... 
doi:10.1186/1471-2164-13-732 pmid:23270413 pmcid:PMC3560207 fatcat:ku55xicefzasjmvye45inry6bq
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