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https://www.readbyqxmd.com/read/29155860/chip-seq-analysis-identifies-p27-kip1-target-genes-involved-in-cell-adhesion-and-cell-signalling-in-mouse-embryonic-fibroblasts
#1
Atilla Biçer, Serena Orlando, Abul B M M K Islam, Edurne Gallastegui, Arnaud Besson, Rosa Aligué, Oriol Bachs, Maria Jesús Pujol
The protein p27Kip1 (p27), a member of the Cip-Kip family of cyclin-dependent kinase inhibitors, is involved in tumorigenesis and a correlation between reduced levels of this protein in human tumours and a worse prognosis has been established. Recent reports revealed that p27 also behaves as a transcriptional regulator. Thus, it has been postulated that the development of tumours with low amounts of p27 could be propitiated by deregulation of transcriptional programs under the control of p27. However, these programs still remain mostly unknown...
2017: PloS One
https://www.readbyqxmd.com/read/29155508/microarray-bioinformatics-in-cancer-a-review
#2
Ziqi Tao, Aimin Shi, Rui Li, Yiqiu Wang, Xin Wang, Jing Zhao
Bioinformatics is one of the newest fields of biological research, and should be viewed broadly as the use of mathematical, statistical, and computational methods for the processing and analysis of biological data. Over the last decade, the rapid growth of information and technology in both "genomics" and "omics" eras has been overwhelming for the laboratory scientists to process experimental results. Traditional gene-by-gene approaches in research are insufficient to meet the growth and demand of biological research in understanding the true biology...
July 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29153527/short-communication-genomic-prediction-using-imputed-whole-genome-sequence-variants-in-brown-swiss-cattle
#3
Mirjam Frischknecht, Theodorus H E Meuwissen, Beat Bapst, Franz R Seefried, Christine Flury, Dorian Garrick, Heidi Signer-Hasler, Christian Stricker, Anna Bieber, Ruedi Fries, Ingolf Russ, Johann Sölkner, Alessandro Bagnato, Birgit Gredler-Grandl
The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies...
November 15, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29149270/aniseed-2017-extending-the-integrated-ascidian-database-to-the-exploration-and-evolutionary-comparison-of-genome-scale-datasets
#4
Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Magali Naville, Kazuhiro R Nitta, Jacques Piette, Wendy Reeves, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah K Lowe, Mickael Mendez, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C Titus Brown, Christian Cambillau, Lionel Christiaen, Frédéric Delsuc, Emmanuel Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie Swalla, Michael Veeman, Jean-Nicolas Volff, Patrick Lemaire
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29146583/comparison-of-chip-seq-data-and-a-reference-motif-set-for-human-krab-c2h2-zinc-finger-proteins
#5
Marjan Barazandeh, Sam Lambert, Mihai Albu, Timothy R Hughes
KRAB C2H2 zinc finger proteins (KZNFs) are the largest and most diverse family of human transcription factors, likely due to diversifying selection driven by novel endogenous retroelements (EREs), but the vast majority lack binding motifs or functional data. Two recent studies analyzed a majority of the human KZNFs using either ChIP-seq (60 proteins) or ChIP-exo (221 proteins) in the same cell type (HEK293). The ChIP-exo paper did not describe binding motifs, however. Thirty-nine proteins are represented in both studies, enabling the systematic comparison of the data sets presented here...
November 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29145608/medreaders-a-database-for-transcription-factors-that-bind-to-methylated-dna
#6
Guohua Wang, Ximei Luo, Jianan Wang, Jun Wan, Shuli Xia, Heng Zhu, Jiang Qian, Yadong Wang
Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29140464/hocomoco-towards-a-complete-collection-of-transcription-factor-binding-models-for-human-and-mouse-via-large-scale-chip-seq-analysis
#7
Ivan V Kulakovskiy, Ilya E Vorontsov, Ivan S Yevshin, Ruslan N Sharipov, Alla D Fedorova, Eugene I Rumynskiy, Yulia A Medvedeva, Arturo Magana-Mora, Vladimir B Bajic, Dmitry A Papatsenko, Fedor A Kolpakov, Vsevolod J Makeev
We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138344/targeting-the-mycn-parp-dna-damage-response-pathway-inneuroendocrine-prostate-cancer
#8
Wei Zhang, Bo Liu, Wenhui Wu, Likun Li, Bradley M Broom, Spyridon M Basourakos, Dimitrios Korentzelos, Yang Luan, Jianxiang Wang, Guang Yang, Sanghee Park, Abul K Azad, Xuhong Cao, Jeri Kim, Paul Corn, Christopher Logothetis, Ana M Aparicio, Arul M Chinnayan, Nora M Navone, Patricia Troncoso, Timothy C Thompson
PURPOSE: We investigated MYCN-regulated molecular pathways in castration-resistant prostate cancer (CRPC) classified by morphological criteria as adenocarcinoma or neuroendocrine to extend the molecular phenotype, establish driver pathways, and identify novel approaches to combination therapy for NEPC. RESULTS: Using comparative bioinformatics analyses of CRPC-Adeno and CRPC-Neuro RNA sequence data from public datasets and a panel of 28 PDX models we identified a MYCN-PARP-DNA damage response (DDR) pathway that is enriched in CRPC with neuroendocrine differentiation (NED) and CRPC-Neuro...
November 14, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#9
Oluwatosin Oluwadare, Jianlin Cheng
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29134420/co-localization-and-interaction-of-pax5-with-iba1-in-brain-of-mice
#10
Shashank Kumar Maurya, Rajnikant Mishra
The Pax5, a B-cell-Specific Activator Protein (BSAP) and redox-sensitive transcription factor, is expressed in the immune-privileged brain, B-lymphocytes, lymph nodes and spleen. PAX5-mediated immune pathway has also been described in the progression of Glioblastoma multiforme. However, the status of Pax5 and its role in brain immunity are not yet elucidated. In silico analysis of Pax5 interacting proteins predicts its interaction with proteins of cell proliferation, differentiation of hematopoietic cells, neurogenesis and several cell signalling pathways...
November 13, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/29133016/dynamic-transcriptional-control-of-macrophage-mirna-signature-via-inflammation-responsive-enhancers-revealed-using-a-combination-of-next-generation-sequencing-based-approaches
#11
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29129639/determinants-of-histone-h3k4-methylation-patterns
#12
Luis M Soares, P Cody He, Yujin Chun, Hyunsuk Suh, TaeSoo Kim, Stephen Buratowski
Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene expression. This methylation "gradient" is thought to result from preferential binding of the H3K4 methyltransferase Set1/complex associated with Set1 (COMPASS) to promoter-proximal RNA polymerase II. However, other studies have suggested that location-specific cues allosterically activate Set1. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments show that H3K4 methylation patterns on active genes are not universal or fixed and change in response to both transcription elongation rate and frequency as well as reduced COMPASS activity...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29126153/an-empirical-bayes-test-for-allelic-imbalance-detection-in-chip-seq
#13
Qi Zhang, Sündüz Keles
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has enabled discovery of genomic regions enriched with biological signals such as transcription factor binding and histone modifications. Allelic-imbalance (ALI) detection is a complementary analysis of ChIP-seq data for associating biological signals with single nucleotide polymorphisms (SNPs). It has been successfully used in elucidating functional roles of non-coding SNPs. Commonly used statistical approaches for ALI detection are often based on binomial testing and mixture models, both of which rely on strong assumptions on the distribution of the unobserved allelic probability, and have significant practical shortcomings...
November 3, 2017: Biostatistics
https://www.readbyqxmd.com/read/29126132/cost-effective-and-accurate-method-of-measuring-fetal-fraction-using-snp-imputation
#14
Minjeong Kim, Jai-Hoon Kim, Kangseok Kim, Sunshin Kim
Motivation: With the discovery of cell-free fetal DNA in maternal blood, the demand for non-invasive prenatal testing (NIPT) has been increasing. To obtain reliable NIPT results, it is important to accurately estimate the fetal fraction. In this study, we propose an accurate and cost-effective method for measuring fetal fractions using single-nucleotide polymorphisms (SNPs). Results: A total of 84 samples were sequenced via semiconductor sequencing using a 0.3x sequencing coverage...
November 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29119388/potentialities-of-microrna-diagnosis-in-patients-with-bladder-cancer
#15
P V Shegay, A A Zhavoronkov, N M Gaifullin, N V Vorob'ev, B Ya Alekseev, S V Popov, A V Garazha, A A Buzdin, A D Kaprin
Despite promising vista of the use of microRNA in molecular diagnosis of bladder cancer, there are few data on their expression profiles, which impedes assessment of diagnostic value of these marker molecules. In this study, suppression subtractive hybridization, on-chip hybridization, and high-throughput deep sequencing focused on profiling microRNA and assessing the diagnostic value of revealed marker molecules.
November 9, 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29118739/resolving-species-level-changes-in-a-representative-soil-bacterial-community-using-microfluidic-quantitative-pcr
#16
Hannah Kleyer, Robin Tecon, Dani Or
Rapid advances in genome sequencing technologies enable determination of relative bacterial abundances and community composition, yet, changes at the species level remain difficult to detect despite importance for certain ecological inferences. We present a method for extraction and direct quantification of species composition of a predefined multispecies bacterial community using microfluidic-based quantitative real-time PCR (qPCR). We employ a nested PCR approach based on universal 16S rRNA gene pre-amplification followed by detection and quantification of absolute abundance of bacterial species using microfluidic array of parallel singleplex qPCR reactions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29116820/gsmc-combining-parallel-gibbs-sampling-with-maximal-cliques-for-hunting-dna-motif
#17
Chao Pei, Shu-Lin Wang, Jianwen Fang, Wei Zhang
Regulatory elements are responsible for regulating gene transcription. Therefore, identification of these elements is a tremendous challenge in the field of gene expression. Transcription factors (TFs) play a key role in gene regulation by binding to target promoter sequences. A set of conserved sequence patterns with a highly similar structure that is bound by a TF is called a motif. Motif discovery has been a difficult problem over the past decades. Meanwhile, it is a foundation stone in meeting this challenge...
November 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29115919/high-resolution-analysis-of-selection-sweeps-identified-between-fine-wool-merino-and-coarse-wool-churra-sheep-breeds
#18
Beatriz Gutiérrez-Gil, Cristina Esteban-Blanco, Pamela Wiener, Praveen Krishna Chitneedi, Aroa Suarez-Vega, Juan-Jose Arranz
BACKGROUND: With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep...
November 7, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29114022/hupb-is-a-bacterial-nucleoid-associated-protein-with-an-indispensable-eukaryotic-like-tail
#19
Joanna Hołówka, Damian Trojanowski, Katarzyna Ginda, Bartosz Wojtaś, Bartłomiej Gielniewski, Dagmara Jakimowicz, Jolanta Zakrzewska-Czerwińska
In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organized and yet dynamic chromosome structure, the HU protein is one of the most conserved and highly abundant. HupB, a homologue of HU, was recently identified in mycobacteria. This intriguing mycobacterial NAP is composed of two domains: an N-terminal domain that resembles bacterial HU, and a long and distinctive C-terminal domain that contains several PAKK/KAAK motifs, which are characteristic of the H1/H5 family of eukaryotic histones...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29114019/native-elongating-transcript-sequencing-reveals-global-anti-correlation-between-sense-and-antisense-nascent-transcription-in-fission-yeast
#20
Maxime Wery, Camille Gautier, Marc Descrimes, Mayuko Yoda, Hervé Vennin-Rendos, Valérie Migeot, Daniel Gautheret, Damien Hermand, Antonin Morillon
Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site...
November 7, 2017: RNA
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