microRNA sequencing data analysis

Question

[Bei.Liu]

I am analyzing the microRNA sequencing data, and the company have done some standard analysis for me but not enough.

I have got the targets of the microRNAs, and the targets have been gene ontology and divided into different functional groups, I am interested in the targets which have been grouped into the "stress response" process, I am not sure whether my thought is correct,but I want to know how I can find the specific microRNAs for these targets which related to the stress response.

thank you

Answer 1

[natasha.sernova]

What organisms do you study?

There are a lot of papers for stress-response in case of different human diseases, for example.

I may suggest several articles but I am not sure that's enough and they satisfy your needs.

A general review (2010):

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996264/

human atherosclerosis:

http://www.nature.com/nrcardio/journal/v12/n6/full/nrcardio.2015.38.html

MicroRNAs and epigenetic regulation of the stress response, Neurobiology of stress:

http://www.weizmann.ac.il/neurobiology/labs/chen/research-activities/micrornas-and-epigenetic-regulation-stress-response

MicroRNAs: The Potential Biomarkers in Plant Stress Response:

http://www.scirp.org/journal/PaperInformation.aspx?PaperID=43925

MicroRNA Responses to Cellular Stress, CANCER RESEARCH

http://cancerres.aacrjournals.org/content/66/22/10843

miRNA modulation of the cellular stress response, Future oncology

http://www.futuremedicine.com/doi/abs/10.2217/14796694.4.2.289

[Bei.Liu]

thank you for your help, but I am studying the hordeum vulgare. the company predicted lots of novel microRNAs which I don't think very reliable, so I plan to predict novel microRNAs by myself, can you recommend a software? and now I am very confused about the known and conserved microRNAs, can you explain a little bit ?

Answer 2

[natasha.sernova]

There are some databases of miRNA.

Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317698/

Identification and characterization of microRNAs from barley (Hordeum vulgare L.) by high-throughput sequencing.

http://www.ncbi.nlm.nih.gov/pubmed/22489137

A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.)

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-595

A Database:

"Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing"

http://www.mirbase.org/cgi-bin/reference.pl?medline=22489137

Database tool:

PmiRExAt: plant miRNA expression atlas database and web applications

http://database.oxfordjournals.org/content/2016/baw060.full.pdf

Concerning known and conserved microRNAs:

http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000500010

"Although some miRNAs are known to be conserved throughout the plant kingdom,

the advent of massively parallel DNA sequencing methods allowed the identification of a vast number of non-conserved

genes, even in closely related plants (Rajagopalan et al., 2006; Fahlgren et al., 2007; Ma et al., 2010). To date, there are

about ten thousand mature miRNA sequences of green plants (Viridiplantae) deposited in the miRBase database

(miRBase) (Griffiths-Jones, 2004). However, these sequences are not evenly distributed among the taxa. For example,

information from economically important plants is almost entirely lacking".

Discovery of barley miRNAs through deep sequencing of short reads

http://sci-hub.cc/10.1186/1471-2164-12-129

Boron Stress Responsive MicroRNAs and Their Targets in Barley

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608689/

You would like to have some soft. See this list:

MiRNA and pre-miRNA tools

http://wwwmgs.bionet.nsc.ru/mgs/programs/rnaanalys/mirna_premirna_prediction_tools.html