Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

Ding, Min; Wang, Haiyun; Chen, Jiajia; Shen, Bairong; Xu, Zigang

doi:10.1155/2012/568950

Cited by 7 publications

(5 citation statements)

References 44 publications

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“…ChIP-seq assays have confirmed these evidences as presented in studies of AR in prostate cancer cell [127,128] and of ER [129][130][131], GR [132], and PPAR [133] in breast cancer cells. In these investigations authors found new insights into the DNA sequences, in which ones NRs can bind and identify cooperating transcription factors.…”

Section: Chromatin Immunoprecipitation Sequencing (Chip-seq)supporting

confidence: 65%

Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods

Fattori

Indolfo

Campos

et al. 2014

Nuclear Receptor Research

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Abstract. Nuclear receptors (NRs) comprise a superfamily of proteins modulated by ligands that regulate the expression of target genes. These proteins share a multidomain structure harboring an N-terminal domain, a highly conserved DNA binding domain, and a ligand binding domain, which has ligand dependent activation function. They play key roles in development, metabolism, and physiology being closely related to diseases. Most of the knowledge about this superfamily emerges from investigations on new ligands and are mostly centered in the ligand binding domain. However, more investigation focusing on interactions between DNA and DNA binding domain is necessary to shed light on important roles of NRs' participation in transcriptional mechanisms and in specific genes network. Here, our goal is to discuss some nuances of NRs-DNA interaction, describing details of the most used techniques in this sort of study, such as gel shift (EMSA), DNA footprinting, reporter gene assay, ChIP-Seq, 3C, and fluorescence anisotropy. Additionally, we aim to provide tools, presenting advantages and disadvantages of these common methods, when choosing the most suitable one to study NRs-DNA interactions to answer specific questions.

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Section: Chromatin Immunoprecipitation Sequencing (Chip-seq)supporting

confidence: 65%

Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods

Fattori

Indolfo

Campos

et al. 2014

Nuclear Receptor Research

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“…This algorithm was chosen because (i) it has been designed for multi-class testing among RNA-seq datasets (i.e. allows for more than pair-wise comparisons simultaneously, and can identify over-expression in multiple tissues), (ii) it has been shown to have low bias and false discovery rates relative to other differential expression algorithms for other RNA-seq datasets [22] , [23] , [24] , and (iii) it has demonstrated effectiveness in other studies [21] , [25] , [26] , [27] , [28] . This algorithm identified approximately 69% of the expressed genes as being over-expressed in at least one of the tissues (with p≤0.05 confidence and a false discovery rate of 0.8%).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum

2014

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Background Caenorhabditis elegans has traditionally been used as a model for studying nematode biology, but its small size limits the ability for researchers to perform some experiments such as high-throughput tissue-specific gene expression studies. However, the dissection of individual tissues is possible in the parasitic nematode Ascaris suum due to its relatively large size. Here, we take advantage of the recent genome sequencing of Ascaris suum and the ability to physically dissect its separate tissues to produce a wide-scale tissue-specific nematode RNA-seq datasets, including data on three non-reproductive tissues (head, pharynx, and intestine) in both male and female worms, as well as four reproductive tissues (testis, seminal vesicle, ovary, and uterus). We obtained fundamental information about the biology of diverse cell types and potential interactions among tissues within this multicellular organism.Methodology/Principal FindingsOverexpression and functional enrichment analyses identified many putative biological functions enriched in each tissue studied, including functions which have not been previously studied in detail in nematodes. Putative tissue-specific transcriptional factors and corresponding binding motifs that regulate expression in each tissue were identified, including the intestine-enriched ELT-2 motif/transcription factor previously described in nematode intestines. Constitutively expressed and novel genes were also characterized, with the largest number of novel genes found to be overexpressed in the testis. Finally, a putative acetylcholine-mediated transcriptional network connecting biological activity in the head to the male reproductive system is described using co-expression networks, along with a similar ecdysone-mediated system in the female.Conclusions/SignificanceThe expression profiles, co-expression networks and co-expression regulation of the 10 tissues studied and the tissue-specific analysis presented here are a valuable resource for studying tissue-specific biological functions in nematodes.

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“…Herein, we mapped the genes uniquely regulated by candidate miRNAs to GeneGo database for analysis of enriched signaling pathway and disease ontology [ 40 – 42 ]. GeneGo database was from MetaCore.…”

Section: Methodsmentioning

confidence: 99%

Identification of MicroRNA as Sepsis Biomarker Based on miRNAs Regulatory Network Analysis

Huang

Sun

Yan

et al. 2014

BioMed Research International

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Sepsis is regarded as arising from an unusual systemic response to infection but the physiopathology of sepsis remains elusive. At present, sepsis is still a fatal condition with delayed diagnosis and a poor outcome. Many biomarkers have been reported in clinical application for patients with sepsis, and claimed to improve the diagnosis and treatment. Because of the difficulty in the interpreting of clinical features of sepsis, some biomarkers do not show high sensitivity and specificity. MicroRNAs (miRNAs) are small noncoding RNAs which pair the sites in mRNAs to regulate gene expression in eukaryotes. They play a key role in inflammatory response, and have been validated to be potential sepsis biomarker recently. In the present work, we apply a miRNA regulatory network based method to identify novel microRNA biomarkers associated with the early diagnosis of sepsis. By analyzing the miRNA expression profiles and the miRNA regulatory network, we obtained novel miRNAs associated with sepsis. Pathways analysis, disease ontology analysis, and protein-protein interaction network (PIN) analysis, as well as ROC curve, were exploited to testify the reliability of the predicted miRNAs. We finally identified 8 novel miRNAs which have the potential to be sepsis biomarkers.

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Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

Cited by 7 publications

References 44 publications

Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods

Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods

Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum

Identification of MicroRNA as Sepsis Biomarker Based on miRNAs Regulatory Network Analysis

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