Predictive and Functional Analysis of Long Noncoding RNAs

A novel community driven software for functional enrichment analysis of extracellular vesicles data

Published date : 26 May 2017

Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture “what the community needs in a tool”. Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes.

type
Journal Paper
journal
Journal of Extracellular Vesicles 2017, Vol. 6, 2017, Issue 1, doi: 10.1080/20013078.2017.1321455
Impact Factor
4.259

Genome-wide analysis of mRNAs associated with mouse peroxisomes

Published date : 22 Dec 2016

Background: RNA is often targeted to be localized to the specific subcellular compartments. Specific localization of mRNA is believed to be an important mechanism for targeting their protein products to the locations, where their function is required.

type
Journal Paper
journal
BMC Genomics 2016, 17 (Supp 13), 1028, doi: 10.1186/s12864-016-3330-x
Impact Factor
3.869

Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles

Published date : 22 Dec 2014

Secreted membrane-enclosed vesicles, collectively called extracellular vesicles (EVs), which include exosomes, ectosomes, microvesicles, microparticles, apoptotic bodies and other EV subsets, encompass a very rapidly growing scientific field in biology and medicine. Importantly, it is currently technically challenging to obtain a totally pure EV fraction free from non-vesicular components for functional studies, and therefore there is a need to establish guidelines for analyses of these vesicles and reporting of scientific studies on EV biology.

type
Journal Paper
journal
Journal of Extracellular Vesicles 2014, 3: 26913 - http://dx.doi.org/10.3402/jev.v3.26913

HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

Published date : 08 Dec 2014

Background
Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies.

Results

type
Journal Paper
journal
BMC Genomics 2014, 15(Suppl 9):S7 doi:10.1186/1471-2164-15-S9-S7
Impact Factor
4.04

Overexpression of SMARCE1 is associated with CD8+ T-cell infiltration in eary stage ovarian cancer

Published date : 29 May 2014

T-lymphocyte infiltration in ovarian tumors has been linked to a favorable prognosis, hence, exploring the mechanism of T-cell recruitment in the tumor is warranted. We employed a differential expression analysis to identify genes over-expressed in early stage ovarian cancer samples that contained CD8 infiltrating T-lymphocytes. Among other genes, we discovered that TTF1, a regulator of ribosomal RNA gene expression, and SMARCE1, a factor associated with chromatin remodeling were overexpressed in first stage CD8+ ovarian tumors.

type
Journal Paper
journal
The International Journal of Biochemistry & Cell Biology, 53, 2014, Pg 389-398, doi: 10.1016/j.biocel.2014.05.031

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing

Published date : 05 Nov 2013

Exosomes are nanosized (30-100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics.

type
Journal Paper
journal
PeerJ. 2013 Nov 5, http://dx.doi.org/10.7717/peerj.201

Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3'-untranslated regions

Published date : 07 Jun 2013

Small secreted membrane vesicles called exosomes have recently attracted a great interest after the discovery that they transfer mRNA that can be translated into protein in recipient cells. Surprisingly, we found that for the majority of exosomal mRNAs only a fraction of their corresponding probes is detectable on the expression microarrays. Exosomal mRNA fragmentation is characterized with a specific structural pattern. The closer to the 3′-end of the transcript the fragments are localized, the larger fraction among the secreted RNAs they constitute.

type
Journal Paper
journal
Biology Direct 2013, 8:12, doi:10.1186/1745-6150-8-12
Impact Factor
2.72

Tysnd1 Deficiency in Mice Interferes with the Peroxisomal Localization of PTS2 Enzymes, Causing Lipid Metabolic Abnormalities and Male Infertility

Published date : 14 Feb 2013

Peroxisomes are subcellular organelles involved in lipid metabolic processes, including those of very-long-chain fatty acids and branched-chain fatty acids, among others. Peroxisome matrix proteins are synthesized in the cytoplasm. Targeting signals (PTS or peroxisomal targeting signal) at the C-terminus (PTS1) or N-terminus (PTS2) of peroxisomal matrix proteins mediate their import into the organelle. In the case of PTS2-containing proteins, the PTS2 signal is cleaved from the protein when transported into peroxisomes.

type
Journal Paper
journal
PLOS Genetics, Feb 2013, Vol. 9, Issue 2, doi:10.1371/journal.pgen.1003286
Impact Factor
8.694

ALEX1 suppresses colony formation ability of human colorectal carcinoma cell lines

Published date : 17 May 2012

Arm protein lost in epithelial cancers, on chromosome X (ALEX; also known as armadillo repeat containing, X-linked [ARMCX]) is a novel subgroup within the armadillo (ARM) family, which has several ARM repeat domains. The biological function of classical ARM family members such as β-catenin is well understood, but that of the ALEX/ARMCX family members is largely unknown. Here we evaluate the effects of ALEX1 overexpression on in vitro colony formation ability and expression of ALEX1 mRNA in human colorectal tumor.

type
Journal Paper
journal
Cancer Science 2012, doi: 10.1111/j.1349-7006.2012.02300.x