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Protocols

MiTranscriptome specifications

Information


Unique identifier OMICS_29205
Name MiTranscriptome
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Arul Chinnaiyan

Publication for MiTranscriptome

MiTranscriptome citations

 (16)
library_books

Expression levels of long non coding RNAs are prognostic for AML outcome

2018
PMCID: 5889529
PMID: 29625580
DOI: 10.1186/s13045-018-0596-2

[…] ero gold kit. HTSeq count version 0.6.1 [] was used for gene expression estimation. RNAseq count data normalization was performed using the TMM method []. A total of 3030 lncRNAs were annotated using MiTranscriptome database []. […]

library_books

Liver X Receptor–Binding DNA Motif Associated With Atherosclerosis‐Specific DNA Methylation Profiles of Alu Elements and Neighboring CpG Islands

2018
PMCID: 5850253
PMID: 29386205
DOI: 10.1161/JAHA.117.007686

[…] nome Browser, and the sequence of Alu elements was used as published in Repbase (girinst.org/repbase). Long noncoding RNA (lncRNA) coordinates were obtained from RNA sequencing libraries available in MiTranscriptome (58 648 lncRNAs; mitranscriptome.org). The reference GRCh37/hg19 human genome was used in all cases. The atherosclerotic lesions used in the present study were previously obtained and […]

library_books

Identification and characterization of conserved lncRNAs in human and rat brain

2017
BMC Bioinformatics
PMCID: 5751786
PMID: 29297275
DOI: 10.1186/s12859-017-1890-7

[…] ally, we attained 8150 human and 11,688 rat lncRNAs for conservation analysis. Of the human lncRNAs, 30.8% (2510/8150) overlapped with Ensembl lncRNA, and 95.6% (7791/8150) overlapped with lncRNAs in MiTranscriptome []. MiTranscriptome is a human lncRNA database derived from the computational analysis of RNA-Seq data from various cancer and tissue types and currently does not contain lncRNA annota […]

library_books

Intergenic disease associated regions are abundant in novel transcripts

2017
Genome Biol
PMCID: 5747244
PMID: 29284497
DOI: 10.1186/s13059-017-1363-3

[…] the capture transcript and with a growing proportion over later GENCODE versions, while the more permissive databases such as AceView and ESTs reported 20–30%, with the highest sequence overlap from MiTranscriptome [, , , ] (Fig. ). Next, we measured the coding potential of the captured transcripts with the Coding-Potential Assessment Tool (CPAT) and Coding Potential Calculator (CPC) [, ]. The ma […]

library_books

Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases

2017
PMCID: 5721798
PMID: 29133519
DOI: 10.1161/JAHA.117.007431

[…] criptome meta‐assembly based on cap analysis of gene expression data across 1829 samples from major human primary cell types and tissues as well as transcript models from GENCODE V19, the Cabili set, miTranscriptome, and ENCODE—has defined 27 919 lncRNAs, of which 13 105 were lincRNAs. We found 901 of 2766 of our macrophage lincRNAs overlapped FANTOM CAT lincRNAs within ±250 bp of the TSS (Table ) […]

call_split

Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach

2017
J Proteome Res
PMCID: 5737412
PMID: 28960077
DOI: 10.1021/acs.jproteome.7b00388
call_split See protocol

[…] al.gdc.cancer.gov). The reference genome used for the alignment of the reads was hg19. The annotation of the transcript structures of the human transcriptome considered in this study was derived from MiTranscriptome. This assembly, based on 7256 RNA-Seq experiments from human normal tissues and cancer samples, contains 384 066 predicted transcripts, 165 020 of them corresponding to protein coding […]

Citations

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MiTranscriptome institution(s)
Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA; Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA; Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA; Section of Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI, USA; Department of Statistics, Colorado State University, Fort Collins, CO, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA
MiTranscriptome funding source(s)
Supported in part by the NIH Prostate Specialized Program of Research Excellence grant P50CA69568, the Early Detection Research Network grant UO1 CA111275, US National Institutes of Health R01CA132874, RO1 CA154365, the Department of Defense grant PC100171, the Prostate Cancer Foundation, the Howard Hughes Medical Institute, a Prostate Cancer Foundation Young Investigator Award, the Department of Defense Post-doctoral Fellowship W81XWH-13-1-0284, and a University of Michigan Cellular & Molecular Biology NIGMS Training Grant.

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