What are the software/online tools for miRNA:miRNA and miRNA:mRNA interaction network?

More Hamid Ali Khan's questions See All

Can you help me explain these RNAi results?

We used RNAi to partially silence inhibin and check the effects of this silencing on some genes by qPCR like ERβ, CYP19, CYP11A1, AR, 3βHSD, IGF-I, Kitl, AMH, LHβ and FSHβ . The results indicated...

08 September 2014 6,109 0 View

Can anyone suggest where I can find the complete sequence of HeLa cells ?

As HeLa cells are derived from human cervical cancer cells, does this mean that the genome sequence of Hela cells will be almost similar (means ~ 99%) to human normal human cells (human genome...

02 March 2014 1,973 4 View

If the Star read count and loop read count of a novel miRNA is zero but has some mature read count, can we accept it?

In my deep sequencing data I have some microRNAs with zero star and loop read count but has some mature read count with significant p-value. Can I say that it's a true novel miRNA and should be...

10 November 2013 4,559 4 View

Can we include non-significant data while making a heat-map?

I did deep sequencing for microRNAs using 8 different kind of treatments. Now I am making the heat -map for deferentially expressed microRNAs. Most of the microRNAs having good differential...

09 October 2013 414 6 View

What do these values mean ( -1.79769e+308 or 1.79769e+308 ) in terms of differential expression (log2 fold change)?

While checking for deferentially expressed miRNAs after deep sequencing, i got some strange values like 1.79769e+308 or 1.79769e+308, which i can't understood. The rest of the values are +1, +2,...

09 October 2013 9,368 10 View

Does anyone have an expertise in statistical software "R"?

I am using R software to make heat map for differential expression of microRNAs from deep sequencing data. Following this command e.g. "nba_heatmap

08 September 2013 4,026 2 View

Is there any database for checking the expression of different genes in specific organs/cells?

I am working with miRNAs and their respective target genes in mice but i am not sure whether the respective target genes are expressing in the respective organs/cells or not ?

05 June 2013 5,246 2 View

What is best way to find a precise target for miRNA?

By using different target prediction softwares I am getting lot of targets for a single miRNA which further vary on the basis of software used. So how to finalize a specific target to further...

31 December 2012 7,901 2 View

How to analyse deep sequencing data?

From where I can get the complete information regarding next generation sequence/deep sequencing data analysis ?

07 August 2012 8,487 5 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

How to define an anisotropic material with asymmetric elastic compliance/stiffness matrix in ANSYS APDL?

I need to model an anisotropic material in which the Poisson's ratio ν_12 ≠ ν_21 and so on. Therefore, the elastic compliance matrix wouldn't be a symmetric one. In ANSYS APDL, for TB,ANEL...

09 August 2024 5,048 2 View

Ethylene glycol is newtonian or non newtonian fluid?

Some sources say it is treated as Newtonian as ethylene glycol has a higher viscosity than water, which affects the flow characteristics in simulations. But some also say it is non-Newtonian.

09 August 2024 2,111 2 View

Request Python code?

Request Python code from this article : Gender equity of authorship in pulmonary medicine over the past decade. THANKS!

08 August 2024 6,242 2 View

Who will be moral responsible for the death of thousands of people in the event of an earthquake?

Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...

08 August 2024 6,134 12 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

Zia Rahman

miRscan

genes.mit.edu/mirscan/‎

Xinkun Wang

I'd second Pratik on using TargetScan to predict target protein-coding genes first. From there you can build a network based on literature using CytoScape or IPA or other tools. It would help if you also have mRNA-Seq data from same samples, that way you can find high-confidence target genes that show tight correlation with your miRNAs. The network built on integrated miRNA-mRNA data will also be more reliable.

Beatriz Perez-Villamil

TALASSO software (http://talasso.cnb.csic.es)

Hamid Hamzeiy

You can find some of them in the list provided below:

http://journal.imbio.de/JIBtools/viewtopic.php?f=41&t=121

Thierry P.P. van den Bosch

Ingenuity

Rekins Janky

http://cancerminer.org/

Pancancer miRNA-mRNA associations

Hamid Ali Khan

Thanks every one.

Goldi A Kozloski

Try the DIANA-miRpath site

I. S. Vlachos, N. Kostoulas, T. Vergoulis, G. Georgakilas, M. Reczko, M. Maragkakis, M. D. Paraskevopoulou, K. Prionidis, T. Dalamagas, A. G. Hatzigeorgiou DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways Nucleic Acids Research 2012 (Web server issue)

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpath/index

Jo Vandesompele

For miRNA:mRNA interactions, we have developed microrna body map a couple of years ago (see paper). This resource has now been upgraded to decodeRNA which will be online soon.

Article The microRNA body map: Dissecting microRNA function through ...

Hussein Sabit

I used MirNet and it is pretty good

Pascal Gottmann

https://146.107.176.32/miR-QTL-Scan/ for diabetes and obesity miRNA