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1.   Hierarchical clustering analysis: Genesis Software

2.   miRBase Website:  http://mirbase.org/

3.   microRNA target prediction:

     1) TARGETSCAN-VERT:   http://www.targetscan.org/vert_61/

     2) RNA22-MMU:   https://cm.jefferson.edu/rna22/Precomputed/OptionController?species=MusMusculus&type=mRNA&version=MB18E65v2

     3) MIRDB:   http://mirdb.org/miRDB/index.html

     4) MICRORNA.ORG:   http://www.microrna.org/microrna/getMirnaForm.do

     5) DIANA-MICROT:   http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=site/index

     6) miRTarBase:   http://mirtarbase.mbc.nctu.edu.tw/index.php

4.  UCSC genome Browser:   http://genome.ucsc.edu/cgi-bin/hgGateway

5.  GeneVenn (search overlapped genes):   http://genevenn.sourceforge.net/??

6.  Dictionary:   www.thefreedictionary.com

7.  p-value calculation of correlation analysis: http://www.jeremymiles.co.uk/usingstatistics/chapter8/sigofrexcel.html

8.  Protein Interaction and Structure:   http://string-db.org/cgi/network.pl?taskId=zfvHbwt_gV3r

9.  web resource for known and predicted functional associations between protein post-translational modifications (PTMs) within and between proteins:

     http://ptmcode.embl.de/help.cgi

10.  Protein structure /functional domain Prediction

      1) http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

      2) http://prosite.expasy.org/

11.  Methylation-related primers design:   http://www.urogene.org/methprimer2/

12.  COSMIC: Catalogue Of Somatic Mutations In Cancer—check mutation:  http://cancer.sanger.ac.uk/cosmic

13.  Target Scan—check the microRNA binding sites on genes:   http://www.targetscan.org/

14.  NIH Human Embryonic Stem Cell Registry:  http://grants.nih.gov/stem_cells/registry/current.htm

15.  The human Protein Atlas:   http://www.proteinatlas.org/

16.  Oncomine:    https://www.oncomine.org/resource/login.html

17.  Ingenuity Pathway Analysis:   http://www.ingenuity.com/products/login

18.  Human metabolomics database download:   http://www.hmdb.ca/downloads

19.  Meta cancer:   http://www.metacancer-fp7.eu/index.php?id=354

20.  Ensembl:   http://uswest.ensembl.org/index.html

21.  Align multiple nucleotide sequences:

       1) http://www.ebi.ac.uk/Tools/msa/mafft/

       2) http://www.ebi.ac.uk/Tools/msa/muscle/

22.  Align multiple protein sequences:   http://www.ebi.ac.uk/Tools/msa/clustalo/

23.  Gene Information in mouse:   http://www.informatics.jax.org/


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