=========================================================================================== CCmiR Author: Jun Ding Date: March,23,2016 =========================================================================================== CCmiR is a miRNA-mRNA binding sites prediction tool, which can model the cooperative and competitive binding between all expressed miRNAs. CCmiR is able to predict the binding probability of each miRNA at any given positions of mRNAs. * INSTALLATION -------------------------------------------------------------------------------------------- 1. For Linux user (1) First, you need to install python (recommend: python 2.7.x-64bit), which is already installed by default for most of current Linux systems. If there is no python 2.7 installed, you can download and install python from (http://www.python.org/download/). You can use "python -V" command to check whether python is installed and the version of Python. (2) Second,you also need Tkinter(Python 2) or tkinter(Python 3) module for Python to enable the GUI. You can check (http://tkinter.unpythonic.net/wiki/How_to_install_Tkinter) for installation instructions on Linux. Note: this is optional if you do not use GUI. (3) The following dependent packages are required : a. miRanda Installation instructions for miRnada package (http://www.microrna.org/microrna/faq.do#question8anchor) tar -xvzf {name_of_miRanda_tarfile} for example, tar -xvzf miRanda-aug2010.tar.gz Second, you must configure the code for your platform. Change the default directory to the miranda directory and then use: ./configure --prefix {directory_to_install_to} for example, ./configure --prefix /Users/yourname/miRanda_aug2010 You may omit the --prefix command to build miranda in the current src directory. If the directory specified with --prefix does not yet exist, the make program will attempt to create it. Third, execute make install If you did not specify an install directory, you should simply execute make Then you should have the miRanda execuatble available for use. ---------------------------------------------------------------------- b. ViennaRNA package Installation instructions for ViennRNA package (http://www.tbi.univie.ac.at/RNA/index.html) ------------------------------ You can download and extract corresponding ViennaRNA package from (http://www.tbi.univie.ac.at/RNA/) CD to the the extracted ViennaRNA package directory ./configure sudo make sudo make install ------------------------------- 2. For Windows user (1) First, you need to install python 2.7-64bit, which can be obtained from (https://www.python.org/ftp/python/2.7.9/python-2.7.9.amd64.msi). Please use the python windows installer from the above download package. After finishing downloading, just double click the installer to get python installed. The python Windows installer already included the Tkinter module by default and therefore you do not need to do it manually. (2) The following dependent packages are required : a. miRanda We provided a standlone version of miRanda, you might not need to install it yourself. If for whatever reason, the standlone version miRanda package is not working properly, please find the intallation instruction for ViennRNA package here (http://www.tbi.univie.ac.at/RNA/index.html) b. ViennaRNA package We provided a standlone version of ViennaRNA package, you might not need to install the viennaRNA package youself. If for whatever reason, the standlone version ViennaRNA package is not working properly, please find the intallation instruction for ViennRNA package here (http://www.tbi.univie.ac.at/RNA/index.html) *Execution -------------------------------------------------------------------------------------------------------------------------------------- A. For Linux user (1) Command Line User a. cd to the directory of the software For example, if you put XXXX under your home directory ( "cd /home/YOURNAME/XXXX") YOURNAME is the your home directory name. b. You can run the software by running the script "mirhmm.py" with the following command: ---------------------------------------------------------------------------------------- python mirhmm.py -a Input microRNA sequences, in FASTA Format -b Input mRNA sequences, in FASTA Format. mRNA id should be Ensembl mRNA ID/ RefSeq mRNA ID -c opitional, this provides the miRNA expression information -p # of cpus used -o # of output For example, if we want to predict miRNA-mRNA bindings from the provided example miRNA sequence(miR) and mRNA sequences (mRNAs) located under the directory "example" by Human model, Human.pkl We can use the following command: ---------------------------------------------------------------------------------------- python mirhmm.py -a example/example_mirna -b example/example_mrna -c example_conc -p 4 -o example_out -------------------------------------------------------------------------------------------- (2) GUI user Just double click the XXXX_GUI.py and choose "Run in Terminal", you might need to change the permision of mirhmm_GUI.py by using the following command: --------------------------------------------------- chmod +x mirhmm_GUI.py --------------------------------------------------- B. For Windows user (1) Command Line User a.open prompt window. Open the Command Prompt window by clicking the Start button , clicking All Programs, clicking Accessories, and then clicking Command Prompt. b.cd to the directory of software c.You can run the software by running the script "mirhmm.py" with the following command: python mirhmm.py -a Input microRNA sequences, in FASTA Format -b Input mRNA sequences, in FASTA Format. mRNA id should be Ensembl mRNA ID/ RefSeq mRNA ID -c opitional, this provides the miRNA expression information -p # of cpus used -o # of output For example, if we want to predict miRNA-mRNA bindings from the provided example miRNA sequence(miR) and mRNA sequences (mRNAs) located under the directory "example" by Human model, Human.pkl We can use the following command: ---------------------------------------------------------------------------------------- python mirhmm.py -a example/example_mirna -b example/example_mrna -c example_conc -p 4 -o example_out -------------------------------------------------------------------------------------------- (2) GUI user Just double click the XXXX_GUI.py and choose "Run in Terminal", you might need to change the permision of TarPmiR_GUI.py by using the following command: --------------------------------------------------- chmod +x mirhmm_GUI.py --------------------------------------------------- (2) GUI user Just double Click the mirhmm_GUI.py *Result ---------------------------------------------------------------------------------------------------------------------------------- Result files: (1) X.bp (X will be your input mRNA_name under specified output) output example: 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ... each row represents the binding proabiility of all miRNAs at each position of mRNA. First row represents the first position of mRNA First col represents the unbound probability, second row represents the binding proabability of miRNA 1, 3rd col-> second miRNA etc. the X.png presents the heatmap file for the X.bp (Visualization) -------------------------- When the software is running, you might see "Running..." on the bottom of the GUI, the GUI probably will show "Not Responding", but it's OK. You will see "Done" on the bottom of GUI when results were obtained. (2) X.TM it represents the transition probability between all miRNAs, it can be used to infer the coopeartive miRNAs. For example ----- 0.997546201019 0.000185795489071 0.000310000004483 2.39976516763e-05 0.000301943040267 0.000395967803413 0.000154107703692 0.000313709217676 0.000221838897542 0.000384972101589 0.000161467071116 0.0632301633198 0.936301531567 0.0 0.0 0.0 3.18333002433e-08 0.000467940052747 1.41153119939e-15 0.0 3.33226868643e-07 0.0 0.0611735249589 0.0 0.743938828607 0.00116978455272 6.45140862749e-08 0.00112156663227 2.33664232772e-05 0.000475739018699 8.17945855832e-08 3.88857934811e-14 0.192097043498 0.0498315029596 0.0 0.0183204868858 0.931840026198 2.86024201264e-09 0.0 0.0 0.0 2.00928960928e-09 0.0 7.97908741931e-06 0.0676695138276 0.0 4.30680782236e-13 0.0 0.603421241307 2.17601405722e-05 1.08997843948e-12 3.13618953547e-05 0.328856122828 6.69842537469e-19 1.31938013742e-18 0.0624242701188 1.68075781879e-18 0.000955211318852 0.0 3.29121656437e-06 0.935553996982 1.6397091366e-11 0.00103106319159 1.80481443391e-06 4.01334662483e-08 3.03222076469e-05 0.0617464683301 7.27251402933e-05 1.50951815282e-06 0.0 2.58566361078e-10 5.3732849957e-11 0.938177521253 0.0 2.7688236803e-09 4.42681276615e-13 1.77267717136e-06 0.0625096350383 2.590983285e-18 0.000549186675365 0.0 0.000842138332756 0.00221617612522 0.0 0.932792869671 0.000513150108426 2.29815129126e-11 0.000576844025571 0.0651104690323 0.0 6.89719654807e-11 0.0 0.433204164158 2.08171653285e-05 2.38593212403e-11 2.50319776231e-05 0.501639517196 4.32175209833e-19 3.77885058753e-10 0.0647810278203 1.25157000931e-12 1.01213782102e-16 0.0 1.23244141664e-09 0.00104722186335 3.80085896205e-07 0.0 4.54807499559e-11 0.934171368951 0.0 0.0534545133471 0.0 0.325023386219 0.00161109810942 2.20234360709e-13 0.00113916564088 2.08417057322e-05 0.00242913550599 6.52837833231e-10 3.33103279803e-16 0.616321858819 ------- i,j of this matrix represents the transition probability between hiden state i to j hidden start 0 represents the unbound hidden start k (k>0), represents the k-th miRNA. (3) X.pred It represents the predicted targets for each miRNA -------------------------------- hsa-miR-517c KCNJ2,HOXA5,RTN1 -------------------------------- (4) X.competitive This file presents the competitive microRNA binding For example, ---------------------------------- AOC3 697 hsa-miR-15b,hsa-miR-16 ----------------------------------- It means, hsa-miR-15b and hsa-miR-16 are competitively binding at AOC3 (position 697) (5) X.cooperative This file tells the cooperative miRNAs For example, ------------------- hsa-miR-205 hsa-miR-363 -------------------- It tells that hsa-miR-205 and hsa-miR-363 are cooperative * License & Credits ------------------------------------------------------------------------------------------------- The software is a freely available for academic use. This software is using the following packages: miRanda ViennaRNA It is also available for non-academic use under appropriate licensing. plase contact xiaoman shawn li (xiaoman@mail.ucf.edu) for further information. *Contact info If you are encountering any problem regarding to mirhmm, please refer the manual first. If problem still can not be solved, please feel free to contact us: Jun Ding (jding@cs.ucf.edu) Nancy Haiyan Hu (haihu@cs.ucf.edu) Xiaoman Shawn Li (xiaoman@mail.ucf.edu)