Package TargetScoreData
|
|
|
- Dominic Heath
- 6 years ago
- Views:
Transcription
1 Title TargetScoreData Version Author Yue Li Package TargetScoreData Maintainer Yue Li April 12, 2018 Precompiled and processed mirna-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct mirnas. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each mirna-mrna interaction. Thus, the user can use these static sequencebased scores together with user-supplied tissue/cell-specific fold-change due to mirna overexpression to predict mirna targets using the package TargetScore (download separately) biocviews ExperimentData, RNASeqData, mirnadata License GPL-2 Suggests TargetScore, gplots NeedsCompilation no R topics documented: TargetScoreData-package get_mirna_family_info get_mirna_transfection_data get_precomputed_logfc get_precomputed_targetscores get_targetscanhuman_contextscore get_targetscanhuman_pct get_validated_targets Index 6 TargetScoreData-package Processed human microrna perturbation data from GEO, and sequence information from TargetScan, and targetscore from TargetScore 1
2 2 TargetScoreData-package Details To automate the pipeline of calculating targetscore using targetscore, we compiled, processed and generated mirna-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct mirnas. To our knowledge, this is by far the largest mirna-pertubation data compendium. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each mirnamrna interaction. Thus, the user can use these static sequence-based scores together with usersupplied tissue/cell-specific fold-change due to mirna overexpression to predict mirna targets using targetscore. Package: TargetScoreData Type: Package Version: Date: License: GPL-2 get_targetscanhuman_contextscore: TargetScan context score for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website ( get_targetscanhuman_pct: TargetScan PCT for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website ( get_mirna_family_info: Get mirna family information obtained TargetScanHuman 6 get_precomputed_targetscores: Pre-calculated targetscores for 112 mirnas using logfc and sequence scores from TargetScan context score and PCT from the RData files above. get_precomputed_logfc: We combined all of the logfc data columns into a single N x M matrix for all of the N = RefSeq mrnas (NM_* obtained from UCSC) and M = 286 datasets. Missing data (logfc) for some genes across studies were imputed using impute from impute.knn. get_mirna_transfection_data: Get log fold-changes (logfc) from each study organized in a list with each item corresponding to a mirna. Notably, some mirnas (e.g., hsa-mir-1) appear more than once in the list corresponding to different studies. get_validated_targets: Get validated targets of human mirna obtained from mirtarbase v3.5 Author(s) Yue Li Maintainer: Yue Li <yueli@cs.toronto.edu> References mirtarbase: a database curates experimentally validated microrna-target interactions. (2011). mirtarbase: a database curates experimentally validated microrna-target interactions., 39(Database issue), D doi: /nar/gkq1107 Friedman, R. C., Farh, K. K.-H., Burge, C. B., & Bartel, D. P. (2009). Most mammalian mrnas are conserved targets of micrornas. Genome Research, 19(1), doi: /gr
3 get_mirna_family_info 3 Garcia, D. M., Baek, D., Shin, C., Bell, G. W., Grimson, A., & Bartel, D. P. (2011). Weak seedpairing stability and high target-site abundance decrease the proficiency of lsy-6 and other micror- NAs. Nature structural & molecular biology, 18(10), doi: /nsmb.2115 See Also Please follow the GEO series number to find the references for each microrna-transfection dataset. get_targetscanhuman_contextscore, get_targetscanhuman_pct, get_validated_targets, get_mirna_family_info, get_precomputed_targetscores, get_precomputed_logfc, get_mirna_transfection_d Examples ls("package:targetscoredata") get_mirna_family_info MicroRNA family information Get human mirna family information obtained frin TargetScanHuman 6 website get_mirna_family_info( = system.file("extdata/mir_family_info.txt", package = "TargetScor get_mirna_transfection_data get_mirna_transfection_data Get log fold-changes (logfc) from each study organized in a list with each item corresponding to a mirna. Notably, some mirnas (e.g., hsa-mir-1) appear more than once in the list corresponding to different studies. get_mirna_transfection_data( = system.file("extdata/mirna_transfection_data.rdata", packa
4 4 get_targetscanhuman_contextscore get_precomputed_logfc get_precomputed_logfc We combined all of the logfc data columns into a single N x M matrix for all of the N = RefSeq mrnas (NM_* obtained from UCSC) and M = 286 datasets. Missing data (logfc) for some genes across studies were imputed using impute from impute.knn. get_precomputed_logfc( = system.file("extdata/logfc.rdata", package = "TargetScoreData")) get_precomputed_targetscores get_precomputed_targetscores Pre-calculated targetscores for 112 mirnas using logfc and sequence scores from TargetScan context score and PCT from the RData files above. get_precomputed_targetscores( = system.file("extdata/targetscores.rdata", package = "Targ get_targetscanhuman_contextscore get_targetscanhuman_contextscore TargetScan context score for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website ( get_targetscanhuman_contextscore( = system.file("extdata/targetscanhuman_contextscore.rda
5 get_targetscanhuman_pct 5 get_targetscanhuman_pct get_targetscanhuman_pct TargetScan PCT for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website ( get_targetscanhuman_pct( = system.file("extdata/targetscanhuman_pct.rdata", package = "Ta get_validated_targets get_validated_targets Get validated targets of human mirna obtained from mirtarbase v3.5 get_validated_targets( = system.file("extdata/hsa_mti.xls", package = "TargetScoreData"))
6 Index Topic data package TargetScoreData-package, 1 get_mirna_family_info, 3, 3 get_mirna_transfection_data, 3, 3 get_precomputed_logfc, 3, 4 get_precomputed_targetscores, 3, 4 get_targetscanhuman_contextscore, 3, 4 get_targetscanhuman_pct, 3, 5 get_validated_targets, 3, 5 targetscore, 2 TargetScoreData (TargetScoreData-package), 1 TargetScoreData-package, 1 6
Package diggitdata. April 11, 2019
Type Package Title Example data for the diggit package Version 1.14.0 Date 2014-08-29 Author Mariano Javier Alvarez Package diggitdata April 11, 2019 Maintainer Mariano Javier Alvarez
NIH Public Access Author Manuscript Nat Struct Mol Biol. Author manuscript; available in PMC 2012 April 01.
NIH Public Access Author Manuscript Published in final edited form as: Nat Struct Mol Biol. ; 18(10): 1139 1146. doi:10.1038/nsmb.2115. Weak Seed-Pairing Stability and High Target-Site Abundance Decrease
Supplementary information for: Human micrornas co-silence in well-separated groups and have different essentialities
Supplementary information for: Human micrornas co-silence in well-separated groups and have different essentialities Gábor Boross,2, Katalin Orosz,2 and Illés J. Farkas 2, Department of Biological Physics,
From mirna regulation to mirna - TF co-regulation: computational
From mirna regulation to mirna - TF co-regulation: computational approaches and challenges 1,* Thuc Duy Le, 1 Lin Liu, 2 Junpeng Zhang, 3 Bing Liu, and 1,* Jiuyong Li 1 School of Information Technology
User Guide. Association analysis. Input
User Guide TFEA.ChIP is a tool to estimate transcription factor enrichment in a set of differentially expressed genes using data from ChIP-Seq experiments performed in different tissues and conditions.
Package DeconRNASeq. November 19, 2017
Type Package Package DeconRNASeq November 19, 2017 Title Deconvolution of Heterogeneous Tissue Samples for mrna-seq data Version 1.20.0 Date 2013-01-22 Author Ting Gong Joseph D. Szustakowski
Analysis of paired mirna-mrna microarray expression data using a stepwise multiple linear regression model
Analysis of paired mirna-mrna microarray expression data using a stepwise multiple linear regression model Yiqian Zhou 1, Rehman Qureshi 2, and Ahmet Sacan 3 1 Pure Storage, 650 Castro Street, Suite #260,
Impact of mirna Sequence on mirna Expression and Correlation between mirna Expression and Cell Cycle Regulation in Breast Cancer Cells
Impact of mirna Sequence on mirna Expression and Correlation between mirna Expression and Cell Cycle Regulation in Breast Cancer Cells Zijun Luo 1 *, Yi Zhao 1, Robert Azencott 2 1 Harbin Institute of
microrna analysis Merete Molton Worren Ståle Nygård
microrna analysis Merete Molton Worren Ståle Nygård Help personnel: Daniel Vodak Background Dysregulation of mirna expression has been connected to progression and development of atherosclerosis The hypothesis:
Using expression profiling data to identify human microrna targets
Using expression profiling data to identify human microrna targets Jim C Huang 1,7, Tomas Babak 2,7, Timothy W Corson 2,3,6, Gordon Chua 4, Sofia Khan 3, Brenda L Gallie 2,3, Timothy R Hughes 2,4, Benjamin
Gene-microRNA network module analysis for ovarian cancer
Gene-microRNA network module analysis for ovarian cancer Shuqin Zhang School of Mathematical Sciences Fudan University Oct. 4, 2016 Outline Introduction Materials and Methods Results Conclusions Introduction
Package inote. June 8, 2017
Type Package Package inote June 8, 2017 Title Integrative Network Omnibus Total Effect Test Version 1.0 Date 2017-06-05 Author Su H. Chu Yen-Tsung Huang
DeSigN: connecting gene expression with therapeutics for drug repurposing and development. Bernard lee GIW 2016, Shanghai 8 October 2016
DeSigN: connecting gene expression with therapeutics for drug repurposing and development Bernard lee GIW 2016, Shanghai 8 October 2016 1 Motivation Average cost: USD 1.8 to 2.6 billion ~2% Attrition rate
Package leukemiaseset
Package leukemiaseset August 14, 2018 Type Package Title Leukemia's microarray gene expression data (expressionset). Version 1.16.0 Date 2013-03-20 Author Sara Aibar, Celia Fontanillo and Javier De Las
Deciphering the Role of micrornas in BRD4-NUT Fusion Gene Induced NUT Midline Carcinoma
www.bioinformation.net Volume 13(6) Hypothesis Deciphering the Role of micrornas in BRD4-NUT Fusion Gene Induced NUT Midline Carcinoma Ekta Pathak 1, Bhavya 1, Divya Mishra 1, Neelam Atri 1, 2, Rajeev
The Characterization of microrna-mediated Gene Regulation as Impacted by Both Target Site Location and Seed Match Type
The Characterization of microrna-mediated Gene Regulation as Impacted by Both Target Site Location and Seed Match Type Wenlong Xu 1, Zixing Wang 1, Yin Liu 1,2 * 1 Department of Neurobiology and Anatomy,
Inferring condition-specific mirna activity from matched mirna and mrna expression data
Inferring condition-specific mirna activity from matched mirna and mrna expression data Junpeng Zhang 1, Thuc Duy Le 2, Lin Liu 2, Bing Liu 3, Jianfeng He 4, Gregory J Goodall 5 and Jiuyong Li 2,* 1 Faculty
mirna-guided regulation at the molecular level
molecular level Hervé Seitz IGH du CNRS, Montpellier, France March 3, 2016 microrna target prediction . microrna target prediction mirna: target: 2 7 5 N NNNNNNNNNNNNNN 3 NNNNNN the seed microrna target
SUPPLEMENTAY FIGURES AND TABLES
SUPPLEMENTAY FIGURES AND TABLES Supplementary Figure S1: Validation of mir expression by quantitative real-time PCR and time course studies on mir- 29a-3p and mir-210-3p. A. The graphs illustrate the expression
Prediction of micrornas and their targets
Prediction of micrornas and their targets Introduction Brief history mirna Biogenesis Computational Methods Mature and precursor mirna prediction mirna target gene prediction Summary micrornas? RNA can
From reference genes to global mean normalization
From reference genes to global mean normalization Jo Vandesompele professor, Ghent University co-founder and CEO, Biogazelle qpcr Symposium USA November 9, 2009 Millbrae, CA outline what is normalization
SUPPLEMENTARY FIGURE LEGENDS
SUPPLEMENTARY FIGURE LEGENDS Supplementary Figure 1 Negative correlation between mir-375 and its predicted target genes, as demonstrated by gene set enrichment analysis (GSEA). 1 The correlation between
How To Use MiRSEA. Junwei Han. July 1, Overview 1. 2 Get the pathway-mirna correlation profile(pmset) and a weighting matrix 2
How To Use MiRSEA Junwei Han July 1, 2015 Contents 1 Overview 1 2 Get the pathway-mirna correlation profile(pmset) and a weighting matrix 2 3 Discovering the dysregulated pathways(or prior gene sets) based
Human breast milk mirna, maternal probiotic supplementation and atopic dermatitis in offsrping
Human breast milk mirna, maternal probiotic supplementation and atopic dermatitis in offsrping Melanie Rae Simpson PhD candidate Department of Public Health and General Practice Norwegian University of
mirna-target prediction based on transcriptional regulation
RESEARCH mirna-target prediction based on transcriptional regulation Toyofumi Fujiwara 1, Tetsushi Yada 2* From ISCB-Asia 2012 Shenzhen, China. 17-19 December 2012 Open Access Abstract Background: micrornas
a) List of KMTs targeted in the shrna screen. The official symbol, KMT designation,
Supplementary Information Supplementary Figures Supplementary Figure 1. a) List of KMTs targeted in the shrna screen. The official symbol, KMT designation, gene ID and specifities are provided. Those highlighted
HALLA KABAT * Outreach Program, mircore, 2929 Plymouth Rd. Ann Arbor, MI 48105, USA LEO TUNKLE *
CERNA SEARCH METHOD IDENTIFIED A MET-ACTIVATED SUBGROUP AMONG EGFR DNA AMPLIFIED LUNG ADENOCARCINOMA PATIENTS HALLA KABAT * Outreach Program, mircore, 2929 Plymouth Rd. Ann Arbor, MI 48105, USA Email:
Package bionetdata. R topics documented: February 19, Type Package Title Biological and chemical data networks Version 1.0.
Type Package Title Biological and chemical data networks Version 1.0.1 Date 2014-09-07 Package bionetdata February 19, 2015 Author Matteo Re, Giorgio Valentini -- Universita' degli Studi di Milano Maintainer
MicroRNA target gene prediction of ischemic stroke by using variational Bayesian inference for Gauss mixture model
EXPERIMENTAL AND THERAPEUTIC MEDICINE MicroRNA target gene prediction of ischemic stroke by using variational Bayesian inference for Gauss mixture model JUN WU 1, BIN WANG 2, JU ZHOU 2 and FAJING JI 3
Cross species analysis of genomics data. Computational Prediction of mirnas and their targets
02-716 Cross species analysis of genomics data Computational Prediction of mirnas and their targets Outline Introduction Brief history mirna Biogenesis Why Computational Methods? Computational Methods
Package mirlab. R topics documented: June 29, Type Package
Type Package Package mirlab June 29, 2018 Title Dry lab for exploring mirna-mrna relationships Version 1.10.0 Date 2016-01-05 Author Thuc Duy Le, Junpeng Zhang Maintainer Thuc Duy Le
Micro-RNA web tools. Introduction. UBio Training Courses. mirnas, target prediction, biology. Gonzalo
Micro-RNA web tools UBio Training Courses Gonzalo Gómez//ggomez@cnio.es Introduction mirnas, target prediction, biology Experimental data Network Filtering Pathway interpretation mirs-pathways network
Package MethPed. September 1, 2018
Type Package Version 1.8.0 Date 2016-01-01 Package MethPed September 1, 2018 Title A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes Depends R (>= 3.0.0), Biobase
Supplementary Materials for
www.sciencesignaling.org/cgi/content/full/8/406/ra126/dc1 Supplementary Materials for The microrna mir-485 targets host and influenza virus transcripts to regulate antiviral immunity and restrict viral
Comparison of open chromatin regions between dentate granule cells and other tissues and neural cell types.
Supplementary Figure 1 Comparison of open chromatin regions between dentate granule cells and other tissues and neural cell types. (a) Pearson correlation heatmap among open chromatin profiles of different
Package AbsFilterGSEA
Type Package Package AbsFilterGSEA September 21, 2017 Title Improved False Positive Control of Gene-Permuting GSEA with Absolute Filtering Version 1.5.1 Author Sora Yoon Maintainer
Functions of microrna in response to cocaine stimulation
Functions of microrna in response to cocaine stimulation L.-F. Xu, J. Wang, F.B. Lv and Q. Song Department of Anesthesiology, Jinan Military General Hospital, Jinan, Shandong Province, China Corresponding
RmiR package vignette
RmiR package vignette Francesco Favero * October 17, 2016 Contents 1 Introduction 1 2 Coupling mirna and gene expression data 2 2.1 Default parameters.............................. 3 2.2 Change the at.least
Paternal exposure and effects on microrna and mrna expression in developing embryo. Department of Chemical and Radiation Nur Duale
Paternal exposure and effects on microrna and mrna expression in developing embryo Department of Chemical and Radiation Nur Duale Our research question Can paternal preconceptional exposure to environmental
Hepatocellular carcinoma (HCC) is among the leading
MiR-940 inhibits hepatocellular carcinoma growth and correlates with prognosis of hepatocellular carcinoma patients Bo Yuan, 1 Yasha Liang, 1 Duoning Wang and Fengming Luo Department of General Practice,
How to use MiRaGE Package
How to use MiRaGE Package Y-h. Taguchi January 4, 2019 Contents 1 Introduction 1 2 Background 2 3 Quick start 4 4 Data Structure 4 4.1 Input: target gene expression........................ 4 4.2 Output:
Package pepdat. R topics documented: March 7, 2015
Package pepdat March 7, 2015 Type Package Title Peptide microarray data package Version 1.0.0 Author Renan Sauteraud, Raphael Gottardo Maintainer Renan Sauteraud Date 2012-08-14 Provides
Package xseq. R topics documented: September 11, 2015
Package xseq September 11, 2015 Title Assessing Functional Impact on Gene Expression of Mutations in Cancer Version 0.2.1 Date 2015-08-25 Author Jiarui Ding, Sohrab Shah Maintainer Jiarui Ding
Computational Analysis of mirna and Target mrna Interactions: Combined Effects of The Quantity and Quality of Their Binding Sites *
www.pibb.ac.cn!"#$%!""&'( Progress in Biochemistry and Biophysics 2009, 36(5): 608~615 Computational Analysis of mirna and Target mrna Interactions: Combined Effects of The Quantity and Quality of Their
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Package CLL. April 19, 2018
Type Package Title A Package for CLL Gene Expression Data Version 1.19.0 Author Elizabeth Whalen Package CLL April 19, 2018 Maintainer Robert Gentleman The CLL package contains the
Integrated network analysis reveals distinct regulatory roles of transcription factors and micrornas
Integrated network analysis reveals distinct regulatory roles of transcription factors and micrornas Yu Guo 1,2,4, Katherine Alexander 1, Andrew G Clark 1, Andrew Grimson 1 and Haiyuan Yu 2,3* 1 Department
Cancer Informatics Lecture
Cancer Informatics Lecture Mayo-UIUC Computational Genomics Course June 22, 2018 Krishna Rani Kalari Ph.D. Associate Professor 2017 MFMER 3702274-1 Outline The Cancer Genome Atlas (TCGA) Genomic Data Commons
High AU content: a signature of upregulated mirna in cardiac diseases
https://helda.helsinki.fi High AU content: a signature of upregulated mirna in cardiac diseases Gupta, Richa 2010-09-20 Gupta, R, Soni, N, Patnaik, P, Sood, I, Singh, R, Rawal, K & Rani, V 2010, ' High
MicroRNA target interactions: new insights from genome-wide approaches
Ann. N.Y. Acad. Sci. ISSN 0077-8923 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES Issue: Nutrition and Physical Activity in Aging, Obesity, and Cancer MicroRNA target interactions: new insights from genome-wide
Supplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63.
Supplementary Figure Legends Supplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63. A. Screenshot of the UCSC genome browser from normalized RNAPII and RNA-seq ChIP-seq data
Tissue and Process Specific microrna mrna Co-Expression in Mammalian Development and Malignancy
Tissue and Process Specific microrna mrna Co-Expression in Mammalian Development and Malignancy The Harvard community has made this article openly available. Please share how this access benefits you.
Bayesian Learning of MicroRNA Targets from Sequence and Expression Data
Bayesian Learning of MicroRNA Targets from Sequence and Expression Data Jim C. Huang 1, Quaid D. Morris 2, Brendan J. Frey 1,2 1 Probabilistic and Statistical Inference Group, University of Toronto 10
Package pathifier. August 17, 2018
Type Package Title Quantify deregulation of pathways in cancer Version 1.19.0 Date 2013-06-27 Author Yotam Drier Package pathifier August 17, 2018 Maintainer Assif Yitzhaky
SUPPLEMENTAL FILE. mir-22 and mir-29a are members of the androgen receptor cistrome modulating. LAMC1 and Mcl-1 in prostate cancer
1 SUPPLEMENTAL FILE 2 3 mir-22 and mir-29a are members of the androgen receptor cistrome modulating LAMC1 and Mcl-1 in prostate cancer 4 5 6 Lorenza Pasqualini 1, Huajie Bu 1,2, Martin Puhr 1, Narisu Narisu
A Quick-Start Guide for rseqdiff
A Quick-Start Guide for rseqdiff Yang Shi (email: shyboy@umich.edu) and Hui Jiang (email: jianghui@umich.edu) 09/05/2013 Introduction rseqdiff is an R package that can detect differential gene and isoform
Long non-coding RNAs
Long non-coding RNAs Dominic Rose Bioinformatics Group, University of Freiburg Bled, Feb. 2011 Outline De novo prediction of long non-coding RNAs (lncrnas) Genome-wide RNA gene-finding Intrinsic properties
Research Article Base Composition Characteristics of Mammalian mirnas
Journal of Nucleic Acids Volume 2013, Article ID 951570, 6 pages http://dx.doi.org/10.1155/2013/951570 Research Article Base Composition Characteristics of Mammalian mirnas Bin Wang Department of Chemistry,
Lentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression.
Supplementary Figure 1 Lentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression. a, Design for lentiviral combinatorial mirna expression and sensor constructs.
How To Use SubpathwayGMir
How To Use SubpathwayGMir Li Feng, Chunquan Li and Xia Li May 20, 2015 Contents 1 Overview 1 2 The experimentally verified mirna-target interactions 2 3 Reconstruct KEGG metabolic pathways 2 3.1 Embed
ivlewbel: Uses heteroscedasticity to estimate mismeasured and endogenous regressor models
ivlewbel: Uses heteroscedasticity to estimate mismeasured and endogenous regressor models Fernihough, A. ivlewbel: Uses heteroscedasticity to estimate mismeasured and endogenous regressor models Queen's
Circular RNAs (circrnas) act a stable mirna sponges
Circular RNAs (circrnas) act a stable mirna sponges cernas compete for mirnas Ancestal mrna (+3 UTR) Pseudogene RNA (+3 UTR homolgy region) The model holds true for all RNAs that share a mirna binding
Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and
Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis Shisong Ma 1,2*, Michael Snyder 3, and Savithramma P Dinesh-Kumar 2* 1 School of Life Sciences, University
Computational Analysis of mrna Expression Profiles Identifies MicroRNA-29a/c as Predictor of Colorectal Cancer Early Recurrence
Computational Analysis of mrna Expression Profiles Identifies MicroRNA-29a/c as Predictor of Colorectal Cancer Early Recurrence Tai-Yue Kuo 1, Edward Hsi 2,4, I-Ping Yang 1,6, Pei-Chien Tsai 1, Jaw-Yuan
DOI: 10.1038/ncb2210 b. ICAM1 ng ml -1 P = 0.0001 Small RNA (15-30nts) ng ml -1 Cell Lysate Exosome HDL Plasma HDL Normal Human HDL mirnas R = 0.45 P < 0.0001 Normal Human Exosome mirnas Figure S1. Characterization
Figure S1: Heat map based on the relative expression of genes and mirnas in human
Figure S1: Heat map based on the relative expression of genes and mirnas in human prostate tissue. Columns represent genes and mirnas; rows represent prostate tissue samples (red squares: Tu samples, green
Synthetic microrna Reference Standards Genomics Research Group ABRF 2015
Synthetic microrna Reference Standards Genomics Research Group ABRF 2015 Don A. Baldwin, Ph.D. support@signalbiology.com Reference samples for Platform evaluation Protocol development Assay service improvement
Small RNA Sequencing. Project Workflow. Service Description. Sequencing Service Specification BGISEQ-500 SERVICE OVERVIEW SAMPLE PREPARATION
BGISEQ-500 SERVICE OVERVIEW Small RNA Sequencing Service Description Small RNAs are a type of non-coding RNA (ncrna) molecules that are less than 200nt in length. They are often involved in gene silencing
Package MSstatsTMT. February 26, Title Protein Significance Analysis in shotgun mass spectrometry-based
Package MSstatsTMT February 26, 2019 Title Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Version 1.1.2 Date 2019-02-25 Tools
Integration of high-throughput biological data
Integration of high-throughput biological data Jean Yang and Vivek Jayaswal School of Mathematics and Statistics University of Sydney Meeting the Challenges of High Dimension: Statistical Methodology,
Patrocles: a database of polymorphic mirna-mediated gene regulation
Patrocles: a database of polymorphic mirna-mediated gene regulation Satellite Eadgene Course "A primer in mirna biology" Liège, 3 march 2008 S. Hiard, D. Baurain, W. Coppieters, X. Tordoir, C. Charlier,
Identification of Key Proteins Associated with Myocardial Infarction using Bioinformatics and Systems Biology
Identification of Key Proteins Associated with Myocardial Infarction using Bioinformatics and Systems Biology Ishtiaque Ahammad 1 * 1. Department of Biochemistry and Microbiology, North South University,
omiras: MicroRNA regulation of gene expression
omiras: MicroRNA regulation of gene expression Sören Müller, Goethe University of Frankfurt am Main Molecular Bioinformatics Group, Institute of Computer Science Plant Molecular Biology Group, Institute
mirna Target Gene Identification: Sourcing mirna Target Gene Relationships for the Analyses of TCGA Illumina MiSeq and RNA-Seq Hiseq Platform Data
Kamla-Raj 2014 Int J Hum Genet, 14(1): 17-22 (2014) mirna Target Gene Identification: Sourcing mirna Target Gene Relationships for the Analyses of TCGA Illumina MiSeq and RNA-Seq Hiseq Platform Data James
mirna Biomarkers Seena K. Ajit PhD Pharmacology & Physiology Drexel University College of Medicine October 12, 2017
mirna Biomarkers Seena K. Ajit PhD Pharmacology & Physiology Drexel University College of Medicine October 12, 2017 Outline Introduction Circulating mirnas as potential biomarkers for pain Complex regional
MicroRNA and Male Infertility: A Potential for Diagnosis
Review Article MicroRNA and Male Infertility: A Potential for Diagnosis * Abstract MicroRNAs (mirnas) are small non-coding single stranded RNA molecules that are physiologically produced in eukaryotic
Table of content. -Supplementary methods. -Figure S1. -Figure S2. -Figure S3. -Table legend
Table of content -Supplementary methods -Figure S1 -Figure S2 -Figure S3 -Table legend Supplementary methods Yeast two-hybrid bait basal transactivation test Because bait constructs sometimes self-transactivate
Package rvtdt. February 20, rvtdt... 1 rvtdt.example... 3 rvtdts... 3 TrendWeights Index 6. population control weighted rare-varaints TDT
Type Package Package rvtdt February 20, 2015 Title population control weighted rare-variants TDT Version 1.0 Date 2014-04-07 Author Yu Jiang, Andrew S. Allen Maintainer Yu Jiang
ABSTRACT INTRODUCTION. Lu Xia 1,*, Daojiang Li 2,*, Changwei Lin 2,3, Shuchun Ou 1, Xiaorong Li 2,3 and Songqing Pan 1.
/, 2017, Vol. 8, (No. 25), pp: 40668-40682 Comparative study of joint bioinformatics analysis of underlying potential of neurimmir, mir-212-3p/mir-132-3p, being involved in epilepsy and its emerging role
Bootstrapped Integrative Hypothesis Test, COPD-Lung Cancer Differentiation, and Joint mirnas Biomarkers
Bootstrapped Integrative Hypothesis Test, COPD-Lung Cancer Differentiation, and Joint mirnas Biomarkers Kai-Ming Jiang 1,2, Bao-Liang Lu 1,2, and Lei Xu 1,2,3(&) 1 Department of Computer Science and Engineering,
An evolutionarily biased distribution of mirna sites toward regulatory genes with high promoter-driven intrinsic transcriptional noise
Zare et al. BMC Evolutionary Biology 2014, 14:74 RESEARCH ARTICLE Open Access An evolutionarily biased distribution of mirna sites toward regulatory genes with high promoter-driven intrinsic transcriptional
Rules for functional microrna targeting
BMB Reports BMB Rep. 2017; 50(11): 554-559 www.bmbreports.org Invited Mini Review Rules for functional microrna targeting Doyeon Kim 1,2, Hee Ryung Chang 1,2 & Daehyun Baek 1,2,3, * 1 Center for RNA Research,
Transcriptome profiling of the developing male germ line identifies the mir-29 family as a global regulator during meiosis
RNA BIOLOGY 2017, VOL. 14, NO. 2, 219 235 http://dx.doi.org/10.1080/15476286.2016.1270002 RESEARCH PAPER Transcriptome profiling of the developing male germ line identifies the mir-29 family as a global
Getting Started.
Getting Started www.scientificbraintrainingpro.com Summary 1. First steps... 2 2. Log in... 2 3. Create an account for a patient... 3 4. Access an exercise with this patient... 4 5. Viewing the results
On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles
On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles Ying-Wooi Wan 1,2,4, Claire M. Mach 2,3, Genevera I. Allen 1,7,8, Matthew L. Anderson 2,4,5 *, Zhandong Liu 1,5,6,7 * 1 Departments of Pediatrics
Package PELVIS. R topics documented: December 18, Type Package
Type Package Package PELVIS December 18, 2018 Title Probabilistic Sex Estimate using Logistic Regression, Based on VISual Traits of the Human Os Coxae Version 1.0.5 Date 2018-12-18 Depends R (>= 3.4.0),
Package PREDAsampledata
Package PREDAsampledata July 17, 2013 Title expression and copy number data on clear cell renal carcinoma samples Version 0.2.7 Author I. Cifola et al. in Cristina Battaglia Lab, University of Milan Sample
Package msgbsr. January 17, 2019
Type Package Package msgbsr January 17, 2019 Title msgbsr: methylation sensitive genotyping by sequencing (MS-GBS) R functions Version 1.6.1 Date 2017-04-24 Author Benjamin Mayne Maintainer Benjamin Mayne
IMPaLA tutorial.
IMPaLA tutorial http://impala.molgen.mpg.de/ 1. Introduction IMPaLA is a web tool, developed for integrated pathway analysis of metabolomics data alongside gene expression or protein abundance data. It
ABSTRACT. mircancer: a microrna-cancer Association Database and Toolkit Based on Text Mining. by Boya Xie. November, 2010
ABSTRACT mircancer: a microrna-cancer Association Database and Toolkit Based on Text Mining by Boya Xie November, 2010 Director: Dr. Qin Ding DEPARTMENT OF COMPUTER SCIENCE MicroRNAs (mirnas) are a class
Mesenchymal stem cells release exosomes that transfer mirnas to endothelial cells and promote angiogenesis
Mesenchymal stem cells release exosomes that transfer mirnas to endothelial cells and promote angiogenesis Tanja Wagner 1 Introduction 2 Mesenchymal stem cells (MSCs) non-haematopoietic, multipotent stem
STEM CELL EPIGENETICS, GENOMICS, AND PROTEOMICS
STEM CELL EPIGENETICS, GENOMICS, AND PROTEOMICS MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries MERAV BAR, a STACIA K. WYMAN, b BRIAN R. FRITZ,
Information resources for healthcare professionals on immunisation schedules and vaccines in EU countries
Information resources for healthcare professionals on immunisation schedules and vaccines in EU countries Tarik Derrough, Surveillance and Response Support Unit, VPD programme, European Centre for Disease
Package ORIClust. February 19, 2015
Type Package Package ORIClust February 19, 2015 Title Order-restricted Information Criterion-based Clustering Algorithm Version 1.0-1 Date 2009-09-10 Author Maintainer Tianqing Liu
Integrated Analysis of Copy Number and Gene Expression
Integrated Analysis of Copy Number and Gene Expression Nexus Copy Number provides user-friendly interface and functionalities to integrate copy number analysis with gene expression results for the purpose
Transcriptome-Wide Prediction of mirna Targets in Human and Mouse Using FASTH
Transcriptome-Wide Prediction of mirna Targets in Human and Mouse Using FASTH Chikako Ragan 1, Nicole Cloonan 1, Sean M. Grimmond 1, Michael Zuker 2, Mark A. Ragan 1 * 1 The University of Queensland, Institute
Supplementary Materials for
www.sciencesignaling.org/cgi/content/full/7/310/ra11/dc1 Supplementary Materials for STAT3 Induction of mir-146b Forms a Feedback Loop to Inhibit the NF-κB to IL-6 Signaling Axis and STAT3-Driven Cancer
USP2 as a potential link between mir-125b and psoriasis
Downloaded from orbit.dtu.dk on: Jan 13, 2019 USP2 as a potential link between mir-125b and psoriasis Wei, T.; Folkersen, Lasse Westergaard; Biskup, E.; Xu, N.; Manfe, V.; Niazi, O.; Gniadecki, R. Published
Simple, rapid, and reliable RNA sequencing
Simple, rapid, and reliable RNA sequencing RNA sequencing applications RNA sequencing provides fundamental insights into how genomes are organized and regulated, giving us valuable information about the
MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals
Resource MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals John Tsang, 1,2 Jun Zhu, 3,4, * and Alexander van Oudenaarden 1, * 1 Department of Physics, Massachusetts