Genome and Gene Expression Data Analysis

Tumor-adjacent tissue co-expression profile analysis reveals pro-oncogenic ribosomal gene signature for prognosis of resectable hepatocellular carcinoma

Currently, molecular markers are not used when determining the prognosis and treatment strategy for patients with hepatocellular carcinoma (HCC). In the present study, we proposed that the identification of common pro-oncogenic pathways in primary tumors (PT) and adjacent non-malignant tissues (AT) typically used to predict HCC patient risks may result in HCC biomarker discovery. We examined the genome-wide mRNA expression profiles of paired PT and AT samples from 321 HCC patients.

type: 
Journal Paper
journal: 
Molecular Oncology, 8 Nov 2017, doi: 10.1002/1878-0261.12153
pubmed: 
29117471
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/29117471
Impact Factor: 
5.314
Date of acceptance: 
2017-10-16

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications.

type: 
Journal Paper
journal: 
Genome Research 2017, 27, Pg 1783-1794, doi: 10.1101/gr.223313.117
pubmed: 
29030469
Url: 
http://genome.cshlp.org/content/27/11/1783.long
Impact Factor: 
11.922

Identification of common oncogenic and early developmental pathways in the ovarian carcinomas controlling by distinct prognostically significant microRNA subsets

BACKGROUND:
High-grade serous ovarian carcinoma (HG-SOC) is the dominant tumor histologic type in epithelial ovarian cancers, exhibiting highly aberrant microRNA expression profiles and diverse pathways that collectively determine the disease aggressiveness and clinical outcomes. However, the functional relationships between microRNAs, the common pathways controlled by the microRNAs and their prognostic and therapeutic significance remain poorly understood.

METHODS:

type: 
Journal Paper
journal: 
BMC Genomics. 2017; 18(Suppl 6): 692, doi: 10.1186/s12864-017-4027-5
pubmed: 
28984201
Url: 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629558/
Impact Factor: 
11.922

Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed.

type: 
Book/Book Chapter
journal: 
Biological Networks and Pathway Analysis, Methods in Molecular Biology, vol. 1613, Pg 193-276, doi: 10.1007/978-1-4939-7027-8_9
pubmed: 
28849563
Url: 
https://www.ncbi.nlm.nih.gov/m/pubmed/28849563/

Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed.

type: 
Book/Book Chapter
journal: 
Biological Networks and Pathway Analysis, Methods in Molecular Biology, Vol. 1613, Pg 193-276, doi: 10.1007/978-1-4939-7027-8_9
pubmed: 
28849563
Url: 
https://www.ncbi.nlm.nih.gov/m/pubmed/28849563/
Date of acceptance: 
2017-12-29

EGF hijacks miR-198/FSTL1 wound-healing switch and steers a two-pronged pathway toward metastasis

Epithelial carcinomas are well known to activate a prolonged wound-healing program that promotes malignant transformation. Wound closure requires the activation of keratinocyte migration via a dual-state molecular switch. This switch involves production of either the anti-migratory microRNA miR-198 or the pro-migratory follistatin-like 1 (FSTL1) protein from a single transcript; miR-198 expression in healthy skin is down-regulated in favor of FSTL1 upon wounding, which enhances keratinocyte migration and promotes re-epithelialization.

type: 
Journal Paper
journal: 
The Journal of Experimental Medicine, 2017,doi: 10.1084/jem.20170354
Url: 
http://jem.rupress.org/content/early/2017/08/18/jem.20170354
Impact Factor: 
11.991
Date of acceptance: 
2017-07-12

Benchmarking selected computational gene network growing tools in context of virus-host interactions

Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens.

type: 
Journal Paper
journal: 
Scientific Reports, 2017 Jul 19;7(1):5805. doi: 10.1038/s41598-017-06020-6
pubmed: 
28724991
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28724991
Impact Factor: 
4.259
Date of acceptance: 
2017-06-07

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

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
Url: 
http://www.tandfonline.com/doi/abs/10.1080/20013078.2017.1321455
Impact Factor: 
4.259

Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification

Robust prognostic gene signatures and therapeutic targets are difficult to derive from expression profiling because of the significant heterogeneity within breast cancer (BC) subtypes. Here, we performed forward genetic screening in mice using Sleeping Beauty transposon mutagenesis to identify candidate BC driver genes in an unbiased manner, using a stabilized N-terminal truncated β-catenin gene as a sensitizer. We identified 134 mouse susceptibility genes from 129 common insertion sites within 34 mammary tumors.

type: 
Journal Paper
journal: 
Proceedings of the National Academy of Sciences of the Unites States of America, PNAS, Vol. 114, No. 11, E2215–E2224, doi: 10.1073/pnas.1701512114
pubmed: 
28251929
Url: 
http://www.pnas.org/content/114/11/E2215.long?tab=author-info
Impact Factor: 
9.661

Mesenchymal Stromal Cells Derived from Human Embryonic Stem Cells, Fetal Limb and Bone Marrow Share a Common Phenotype but Are Transcriptionally and Biologically Different

Mesenchymal stromal cells (MSCs) can be obtained from several sources and the significant differences in their properties make it crucial to investigate the differentiation potential of MSCs from different sources to determine the optimal source of MSCs. We investigated if this biological heterogeneity in MSCs from different sources results in different mechanisms for their differentiation.

type: 
Journal Paper
journal: 
Stem Cell Discovery, 2017, 7, Pg 1-26, doi: 10.4236/scd.2017.71001
Url: 
http://file.scirp.org/Html/1-1080128_77869.htm
Date of acceptance: 
2017-01-20
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