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Mining LINE-1 Characteristics That Mediate Gene Expression
[chapter]
2010
Communications in Computer and Information Science
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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
2014
PLoS ONE
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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
2001
Nature Genetics
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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]
2022
bioRxiv
pre-print
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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
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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]
2006
Lecture Notes in Computer Science
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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
2017
Medicine
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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
2017
OncoTarget
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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
2013
Cancer Research
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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
2003
Molecular and Cellular Biology
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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
2017
Technology in Cancer Research and Treatment
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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
2014
PLoS Genetics
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-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
2014
Science Translational Medicine
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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
2013
Journal of Biological Chemistry
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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-1and 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
2012
BMC Genomics
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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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