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Gene ontology, clustering

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https://www.readbyqxmd.com/read/29343207/genome-wide-analysis-identified-a-number-of-dysregulated-long-noncoding-rna-lncrna-in-human-pancreatic-ductal-adenocarcinoma
#1
Sijie Hao, Lie Yao, Jiaxin Huang, Hang He, Feng Yang, Yang Di, Chen Jin, Deliang Fu
BACKGROUND: Long noncoding RNAs have been shown to play crucial roles in cancer biology, while the long noncoding RNA landscapes of pancreatic ductal adenocarcinoma have not been completely characterized. We aimed to determine whether long noncoding RNA could serve as early diagnostic biomarkers for pancreatic ductal adenocarcinoma. METHOD: We conducted a genome-wide microarray analysis on pancreatic ductal adenocarcinoma and their adjacent noncancerous tissues from 8 Chinese patients...
January 1, 2018: Technology in Cancer Research & Treatment
https://www.readbyqxmd.com/read/29339971/terzyme-a-tool-for-identification-and-analysis-of-the-plant-terpenome
#2
Piyush Priya, Archana Yadav, Jyoti Chand, Gitanjali Yadav
Background: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data...
2018: Plant Methods
https://www.readbyqxmd.com/read/29329292/transcriptome-profiling-with-focus-on-potential-key-genes-for-wing-development-and-evolution-in-megaloprepus-caerulatus-the-damselfly-species-with-the-world-s-largest-wings
#3
Wiebke Feindt, Sara J Oppenheim, Robert DeSalle, Paul Z Goldstein, Heike Hadrys
The evolution, development and coloration of insect wings remains a puzzling subject in evolutionary research. In basal flying insects such as Odonata, genomic research regarding bauplan evolution is still rare. Here we focus on the world's largest odonate species-the "forest giant" Megaloprepus caerulatus, to explore its potential for looking deeper into the development and evolution of wings. A recently discovered cryptic species complex in this genus previously considered monotypic is characterized by morphological differences in wing shape and color patterns...
2018: PloS One
https://www.readbyqxmd.com/read/29328425/bioinformatics-analysis-of-the-cdk2-functions-in-neuroblastoma
#4
Lijuan Bo, Bo Wei, Zhanfeng Wang, Daliang Kong, Zheng Gao, Zhuang Miao
The present study aimed to elucidate the potential mechanism of cyclin-dependent kinase 2 (CDK2) in neuroblastoma progression and to identify the candidate genes associated with neuroblastoma with CDK2 silencing. The microarray data of GSE16480 were obtained from the gene expression omnibus database. This dataset contained 15 samples: Neuroblastoma cell line IMR32 transfected with CDK2 shRNA at 0, 8, 24, 48 and 72 h (n=3 per group; total=15). Significant clusters associated with differentially expressed genes (DEGs) were identified using fuzzy C‑Means algorithm in the Mfuzz package...
December 29, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29322927/cpredictor3-0-detecting-protein-complexes-from-ppi-networks-with-expression-data-and-functional-annotations
#5
Ying Xu, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan
BACKGROUND: Effectively predicting protein complexes not only helps to understand the structures and functions of proteins and their complexes, but also is useful for diagnosing disease and developing new drugs. Up to now, many methods have been developed to detect complexes by mining dense subgraphs from static protein-protein interaction (PPI) networks, while ignoring the value of other biological information and the dynamic properties of cellular systems. RESULTS: In this paper, based on our previous works CPredictor and CPredictor2...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322640/conserved-roles-of-osiris-genes-in-insect-development-polymorphism-and-protection
#6
Chris R Smith, Claire Morandin, Moataz Noureddine, Swati Pant
Much of the variation among insects is derived from the different ways that chitin has been molded to form rigid structures, both internal and external. In this study, we identify a highly conserved expression pattern in an insect-only gene family, the Osiris genes, that is essential for development, but also plays a significant role in phenotypic plasticity and in immunity/toxicity responses. The majority of Osiris genes exist in a highly syntenic cluster, and the cluster itself appears to have arisen very early in the evolution of insects...
January 10, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29319931/metaproteomics-of-colonic-microbiota-unveils-discrete-protein-functions-among-colitic-mice-and-control-groups
#7
Clara Moon, Gregory S Stupp, Andrew I Su, Dennis W Wolan
Metaproteomics can greatly assist established high-throughput sequencing methodologies to provide systems biological insights into the alterations of microbial protein functionalities correlated with disease-associated dysbiosis of the intestinal microbiota. Here, we utilized the well-characterized murine T cell transfer model of colitis to find specific changes within the intestinal luminal proteome associated with inflammation. MS proteomic analysis of colonic samples permitted the identification of ∼10,000-12,000 unique peptides that corresponded to 5,610 protein clusters identified across three groups, including the colitic Rag1-/- T cell recipients, isogenic Rag1-/- controls, and wild-type mice...
January 10, 2018: Proteomics
https://www.readbyqxmd.com/read/29305989/the-immune-response-of-mytilus-edulis-hemocytes-exposed-to-vibrio-splendidus-lgp32-strain-a-transcriptomic-attempt-at-identifying-molecular-actors
#8
Marion Tanguy, Sophie Gauthier-Clerc, Jocelyne Pellerin, Jean-Michel Danger, Ahmed Siah
The marine mussel Mytilus edulis, tolerant to a wide range of environmental changes, combines a key role as a sentinel species for environmental monitoring programs and a significant economic importance. Mortality events caused by infective agents and parasites have not been described in mussels, which suggests an efficient immune system. This study aims at identifying the molecular mechanisms involved in the early immune responses M. edulis' hemocytes challenged with Vibrio splendidus LGP32 strain during 2, 4 and 6 h...
January 3, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29289296/identification-of-differentially-expressed-genes-response-to-tcdd-in-rat-brain-after-long-term-low-dose-exposure
#9
Yangsheng Chen, Li Xu, Heidi Q H Xie, Tuan Xu, Hualing Fu, Songyan Zhang, Rui Sha, Yingjie Xia, Bin Zhao
Several cohort studies have reported that dioxin and dioxin-like polychlorinated biphenyls might impair the nervous system and lead to neurological or neurodegenerative diseases in the elder people, but there is limited research on the involved mechanism. By using microarray analysis, we figured out the differentially expressed genes between brain samples from SD rats after low-dose (0.1μg/(kg▪bw)) dioxin exposure for six months and controls. To investigate the function changes in the course of dioxin exposure, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on the differentially expressed genes...
December 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29286618/cancer-detection-in-microarray-data-using-a-modified-cat-swarm-optimization-clustering-approach
#10
Pandi M, Balamurugan R, Sadhasivam N
Objective: A better understanding of functional genomics can be obtained by extracting patterns hidden in gene expression data. This could have paramount implications for cancer diagnosis, gene treatments and other domains. Clustering may reveal natural structures and identify interesting patterns in underlying data. The main objective of this research was to derive a heuristic approach to detection of highly co-expressed genes related to cancer from gene expression data with minimum Mean Squared Error (MSE)...
December 29, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29286604/protein-protein-interaction-network-analysis-for-a-biomarker-panel-related-to-human-esophageal-adenocarcinoma
#11
Majid Rezaei-Tavirani, Sina Rezaei-Taviran, Mansouri Mansouri, Mohammad Rostami-Nejad, Mostafa Rezaei-Tavirani
Background: Esophageal adenocarcinoma (EAC) is one of the mostlethal cancers in the world with a very poor prognosis. Identification of molecular diagnostic methods is an important goal. Since protein-protein interaction (PPI) network analysis is a suitable method for molecular assessment, in the present research a PPI network related to EAC was targeted. Material and Method: Cytoscape software and its applications including STRING DB, Cluster ONE and ClueGO were applied to analyze the PPI network. Result: Among 182 EAC-related proteins which were identified, 129 were included in a main connected component...
December 29, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29285317/altered-expression-of-differential-gene-and-lncrna-in-the-lower-thoracic-spinal-cord-on-different-time-courses-of-experimental-obstructive-jaundice-model-accompanied-with-altered-peripheral-nociception-in-rats
#12
Qian Wang, Zhi-Xiao Li, Bao-Wen Liu, Zhi-Gang He, Cheng Liu, Min Chen, San-Guang Liu, Wei-Zhong Wu, Hong-Bing Xiang
The spinal origin of jaundice-induced altered peripheral nociceptive response poorly understood. In the current study, we aimed to first validate rats with bile duct ligation (BDL) as a jaundice model accompanied by altered peripheral nociceptive response, and then to analyze differential gene and lncRNA expression patterns in the lower thoracic spinal cord on different time courses after BDL operation by using high-throughput RNA sequencing. The differentially expressed genes (DEGs) identified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, followed by clustering analysis, Gene Ontology analysis and pathway analysis...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29285296/rna-sequencing-reveals-genome-wide-long-non-coding-rnas-profiling-associated-with-early-development-of-diabetic-nephropathy
#13
Wanxin Tang, Dongmei Zhang, Xiaoke Ma
Background: Diabetic nephropathy (DN) seriously threatens the lives of patients, and the mechanism of DN remains largely unknown because of the complex regulation between long non-coding RNA (lncRNA) and protein-coding genes. In early development of diabetic nephropathy (DN), pathogenesis remains largely unknown. Results: We used RNA-sequencing to profile protein-coding and lncRNA gene transcriptome of mouse kidney proximal tubular cells during early stage of DN at various time points...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29283433/congems-condensed-gene-co-expression-module-discovery-through-rule-based-clustering-and-its-application-to-carcinogenesis
#14
Saurav Mallik, Zhongming Zhao
For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures-weighted rank-based Jaccard and Cosine measures-and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s) through the association rule-based learning system and the weighted similarity scores...
December 28, 2017: Genes
https://www.readbyqxmd.com/read/29279524/transcriptional-analysis-of-endothelial-cell-alternation-induced-by-atrial-natriuretic-polypeptide-in-human-umbilical-vein-endothelial-cells
#15
Xuefeng Li, Yu Liang, Zhili Qiao, Jiaoxia Yang, Pengfei Han, Binghai Zhao, Fengxiang Li, Hengjuan Lv, Jifang Guo, Fengmin Gao, Li Li
The aim of this study was to explore how atrial natriuretic polypeptide (ANP) affects the properties and function of endothelial cells. Gene expression data GSE56976 generated at 0, 1, and 6 hours after ANP incubation in human umbilical vein endothelial cells (HUVEC) was used. Microarray data were preprocessed for differentially expressed genes (DEGs) in each time-dependent group. Next, gene ontology (GO), pathway analysis, and transcriptional regulation were performed. Co-expression clustering analysis of DEGs and functional enrichment analysis of co-expression modules were processed...
December 27, 2017: International Heart Journal
https://www.readbyqxmd.com/read/29250158/function-of-mir-25-in-the-invasion-and-metastasis-of-esophageal-squamous-carcinoma-cells-and-bioinformatical-analysis-of-the-mir-106b-25-cluster
#16
Meng Wang, Yangyang Ou Yang, Qingtao Jin, Linlin Shang, Jian Zhang
MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNA molecules that serve a key function in carcinogenesis and tumor progression. Recent evidence indicates that miRNAs may act as powerful regulators of migration and invasion. The present study aimed to investigate the effect of miR-25 on the invasion and metastasis of KYSE-150 and EC109 esophageal squamous cell carcinoma (ESCC) cells, and predict the mechanism of this effect by bioinformatically analyzing the miR-106b-25 cluster. In order to alter the expression of miR-25 in the two cell lines, a miR-25 inhibitor or mimic were transfected into the cells, which were then studied via Transwell migration and invasion assays...
January 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29247800/de-novo-rna-seq-based-transcriptome-analysis-of-papiliotrema-laurentii-strain-ry1-under-nitrogen-starvation
#17
Soumyadev Sarkar, Somnath Chakravorty, Avishek Mukherjee, Debanjana Bhattacharya, Semantee Bhattacharya, Ratan Gachhui
Nitrogen is a key nutrient for all cell forms. Most organisms respond to nitrogen scarcity by slowing down their growth rate. On the contrary, our previous studies have shown that Papiliotrema laurentii strain RY1 has a robust growth under nitrogen starvation. To understand the global regulation that leads to such an extraordinary response, we undertook a de novo approach for transcriptome analysis of the yeast. Close to 33 million sequence reads of high quality for nitrogen limited and enriched condition were generated using Illumina NextSeq500...
December 13, 2017: Gene
https://www.readbyqxmd.com/read/29242905/the-long-noncoding-rna-landscape-of-the-mouse-eye
#18
Weiwei Chen, Shuai Yang, Zhonglou Zhou, Xiaoting Zhao, Jiayun Zhong, Peter S Reinach, Dongsheng Yan
Purpose: Long noncoding RNAs (lncRNAs) are important regulators of diverse biological functions. However, an extensive in-depth analysis of their expression profile and function in mammalian eyes is still lacking. Here we describe comprehensive landscapes of stage-dependent and tissue-specific lncRNA expression in the mouse eye. Methods: Affymetrix transcriptome array profiled lncRNA signatures from six different ocular tissue subsets (i.e., cornea, lens, retina, RPE, choroid, and sclera) in newborn and 8-week-old mice...
December 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29234286/identification-of-biomarkers-correlated-with-the-tnm-staging-and-overall-survival-of-patients-with-bladder-cancer
#19
Sheng Li, Xiaoping Liu, Tongzu Liu, Xiangyu Meng, Xiaohong Yin, Cheng Fang, Di Huang, Yue Cao, Hong Weng, Xiantao Zeng, Xinghuan Wang
Objective: To identify candidate biomarkers correlated with clinical prognosis of patients with bladder cancer (BC). Methods: Weighted gene co-expression network analysis was applied to build a co-expression network to identify hub genes correlated with tumor node metastasis (TNM) staging of BC patients. Functional enrichment analysis was conducted to functionally annotate the hub genes. Protein-protein interaction network analysis of hub genes was performed to identify the interactions among the hub genes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29219805/car-gene-cluster-and-transcript-levels-of-carotenogenic-genes-in-rhodotorula-mucilaginosa
#20
Sara Landolfo, Giuseppe Ianiri, Salvatore Camiolo, Andrea Porceddu, Giuliana Mulas, Rossella Chessa, Giacomo Zara, Ilaria Mannazzu
A molecular approach was applied to the study of the carotenoid biosynthetic pathway of Rhodotorula mucilaginosa. At first, functional annotation of the genome of R. mucilaginosa C2.5t1 was carried out and gene ontology categories were assigned to 4033 predicted proteins. Then, a set of genes involved in different steps of carotenogenesis was identified and those coding for phytoene desaturase, phytoene synthase/lycopene cyclase and carotenoid dioxygenase (CAR genes) proved to be clustered within a region of ~10 kb...
January 2018: Microbiology
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