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This regulatory network was inferred from the input dataset. The miRNAs and mRNAs are presented as round and rectangle nodes respectively. The numerical value popped up upon mouse over the gene node is the log2 transformed fold-change of the gene expression between the two groups. All of the nodes are clickable, and the detailed information of the miRNAs/mRNAs and related cancer pathway will be displayed in another window. The edges between nodes are supported by both interactions (predicted or experimentally verified) and correlations learnt from cancer dataset. The numerical value popped up upon mouse over the edge is the correlation beat value (effect size) between the two nodes. The experimental evidences of the edges reported in previous cancer studies are highlighted by red/orange color. All of these information can be accessed by the "mouse-over" action. This network shows a full map of the miRNA-mRNA regulation of the input gene list(s), and the hub miRNAs (with the high network degree/betweenness centrality) would be the potential cancer drivers or tumor suppressors. The full result table can be accessed in the "Regulations" tab.

"miRNACancerMAP" is also a network visualization tool for users to draw their regulatory network by personal customization. Users can set the complexity of the network by limiting the number of nodes or edges. And the color of the nodes can be defined by different categories of the mRNAs and miRNAs, such as Gene-Ontology, pathway, and expression status. Users can also select to use network degree or network betweenness centrality to define the node size. And edges can be black or colored by the correlation. Purple edge means negative correlation (mostly found between miRNA and mRNA), and blue edge means positive correlation (found in PPI or miRNA-miRNA sponge effect). We can also add the protein-protein interactions (PPI) into the network. This result will show the cluster of genes regulated by some specific miRNAs. Additionally, miRNA-miRNA edges can be added by the "miRNA sponge" button, presenting some clusters of miRNAs that have the interactions via sponge effect.

miRNA-gene regulations

(Download full result)

Num microRNA           Gene miRNA log2FC miRNA pvalue Gene log2FC Gene pvalue Interaction Correlation beta Correlation P-value PMID Reported in cancer studies
1 hsa-miR-125a-3p CIRBP 1.24 1.0E-5 -0.68 0.00013 miRanda -0.13 2.0E-5 NA
2 hsa-miR-24-3p CIRBP 1 0 -0.68 0.00013 miRNAWalker2 validate -0.28 0 NA
3 hsa-miR-338-5p CIRBP -0.58 0.04722 -0.68 0.00013 MirTarget; PITA; miRNATAP -0.14 0 NA
4 hsa-miR-590-3p CIRBP 2.59 0 -0.68 0.00013 miRanda -0.14 0 NA
5 hsa-miR-590-5p CIRBP 3.18 0 -0.68 0.00013 miRanda -0.1 0.00028 NA
6 hsa-miR-629-3p CIRBP 2.37 0 -0.68 0.00013 mirMAP -0.17 0 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 RNA PROCESSING 48 835 2.898e-25 1.348e-21
2 MRNA METABOLIC PROCESS 40 611 4.725e-23 1.099e-19
3 RNA SPLICING VIA TRANSESTERIFICATION REACTIONS 28 267 1.045e-21 1.62e-18
4 MRNA PROCESSING 33 432 4.098e-21 4.767e-18
5 RNA SPLICING 30 367 4.465e-20 4.156e-17
6 RIBONUCLEOPROTEIN COMPLEX BIOGENESIS 27 440 5.076e-15 3.936e-12
7 NLS BEARING PROTEIN IMPORT INTO NUCLEUS 9 22 1.656e-13 1.101e-10
8 NUCLEAR IMPORT 14 129 1.363e-11 7.93e-09
9 PROTEIN FOLDING 17 224 2.737e-11 1.415e-08
10 PROTEIN IMPORT 14 155 1.646e-10 7.588e-08
11 PROTEIN LOCALIZATION TO NUCLEUS 14 156 1.794e-10 7.588e-08
12 NUCLEAR TRANSPORT 19 355 7.236e-10 2.806e-07
13 POSTTRANSCRIPTIONAL REGULATION OF GENE EXPRESSION 21 448 9.725e-10 3.481e-07
14 MITOTIC CELL CYCLE 27 766 1.842e-09 6.122e-07
15 REGULATION OF TELOMERASE RNA LOCALIZATION TO CAJAL BODY 6 15 2.527e-09 7.348e-07
16 POSITIVE REGULATION OF TELOMERASE RNA LOCALIZATION TO CAJAL BODY 6 15 2.527e-09 7.348e-07
17 CELL CYCLE G1 S PHASE TRANSITION 11 111 5.958e-09 1.54e-06
18 G1 S TRANSITION OF MITOTIC CELL CYCLE 11 111 5.958e-09 1.54e-06
19 MULTI ORGANISM TRANSPORT 9 68 1.143e-08 2.66e-06
20 MULTI ORGANISM LOCALIZATION 9 68 1.143e-08 2.66e-06
21 CELL CYCLE PHASE TRANSITION 15 255 1.383e-08 3.064e-06
22 RIBOSOME BIOGENESIS 16 308 2.585e-08 5.428e-06
23 REGULATION OF ESTABLISHMENT OF PROTEIN LOCALIZATION TO CHROMOSOME 5 11 2.683e-08 5.428e-06
24 CELL CYCLE 34 1316 3.277e-08 6.352e-06
25 RIBONUCLEOPROTEIN COMPLEX SUBUNIT ORGANIZATION 13 199 3.863e-08 7.189e-06
26 REGULATION OF RNA STABILITY 11 139 6.303e-08 1.128e-05
27 RRNA METABOLIC PROCESS 14 255 1.008e-07 1.738e-05
28 REGULATION OF PROTEIN LOCALIZATION TO CHROMOSOME TELOMERIC REGION 5 14 1.137e-07 1.89e-05
29 REGULATION OF MRNA METABOLIC PROCESS 10 118 1.334e-07 2.141e-05
30 RNA LOCALIZATION 12 185 1.414e-07 2.193e-05
31 MODULATION BY SYMBIONT OF HOST CELLULAR PROCESS 6 28 1.723e-07 2.586e-05
32 CELL CYCLE PROCESS 29 1081 1.792e-07 2.605e-05
33 PROTEIN LOCALIZATION TO ORGANELLE 20 556 1.999e-07 2.819e-05
34 REGULATION OF DNA REPLICATION 11 161 2.822e-07 3.862e-05
35 POSITIVE REGULATION OF GENE EXPRESSION 38 1733 3.198e-07 4.251e-05
36 REGULATION OF TELOMERE MAINTENANCE VIA TELOMERE LENGTHENING 7 50 3.43e-07 4.433e-05
37 POSITIVE REGULATION OF TELOMERE MAINTENANCE VIA TELOMERE LENGTHENING 6 33 4.876e-07 6.132e-05
38 SPLICEOSOMAL COMPLEX ASSEMBLY 7 53 5.172e-07 6.334e-05
39 NCRNA PROCESSING 16 386 5.59e-07 6.555e-05
40 REGULATION OF CELL CYCLE 26 949 5.635e-07 6.555e-05
41 INTERSPECIES INTERACTION BETWEEN ORGANISMS 21 662 7.648e-07 8.473e-05
42 SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 21 662 7.648e-07 8.473e-05
43 MODULATION BY VIRUS OF HOST MORPHOLOGY OR PHYSIOLOGY 6 37 9.929e-07 0.0001074
44 POSITIVE REGULATION OF DNA REPLICATION 8 86 1.217e-06 0.0001257
45 CELL DIVISION 17 460 1.197e-06 0.0001257
46 ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE 15 361 1.242e-06 0.0001257
47 NCRNA METABOLIC PROCESS 18 533 2.069e-06 0.0002048
48 REGULATION OF TELOMERE MAINTENANCE 7 67 2.62e-06 0.000254
49 RNA SECONDARY STRUCTURE UNWINDING 6 44 2.859e-06 0.0002715
50 REGULATION OF DNA METABOLIC PROCESS 14 340 3.161e-06 0.0002941
51 MODIFICATION BY SYMBIONT OF HOST MORPHOLOGY OR PHYSIOLOGY 6 45 3.274e-06 0.0002987
52 NUCLEIC ACID PHOSPHODIESTER BOND HYDROLYSIS 12 254 4.063e-06 0.0003636
53 POSITIVE REGULATION OF TELOMERE MAINTENANCE 6 47 4.251e-06 0.0003663
54 MACROMOLECULE CATABOLIC PROCESS 24 926 4.173e-06 0.0003663
55 REGULATION OF CELLULAR AMIDE METABOLIC PROCESS 14 354 5.03e-06 0.0004256
56 CELL CYCLE G2 M PHASE TRANSITION 9 138 5.138e-06 0.0004269
57 PROTEIN TARGETING 15 406 5.232e-06 0.0004271
58 MITOTIC NUCLEAR DIVISION 14 361 6.292e-06 0.0005047
59 DNA METABOLIC PROCESS 21 758 6.403e-06 0.000505
60 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 26 1087 6.794e-06 0.0005269
61 RNA STABILIZATION 5 31 8.506e-06 0.0006488
62 MACROMOLECULAR COMPLEX ASSEMBLY 30 1398 1.056e-05 0.0007926
63 SEXUAL REPRODUCTION 20 730 1.269e-05 0.000937
64 NUCLEOBASE CONTAINING COMPOUND TRANSPORT 10 199 1.544e-05 0.001123
65 POSITIVE REGULATION OF DNA BIOSYNTHETIC PROCESS 6 59 1.629e-05 0.001166
66 REGULATION OF TRANSFERASE ACTIVITY 23 946 1.878e-05 0.001324
67 REGULATION OF MRNA SPLICING VIA SPLICEOSOME 6 62 2.172e-05 0.001509
68 REGULATION OF DNA BIOSYNTHETIC PROCESS 7 94 2.506e-05 0.001715
69 NEGATIVE REGULATION OF CELLULAR AMIDE METABOLIC PROCESS 8 131 2.798e-05 0.001887
70 REGULATION OF RNA SPLICING 7 97 3.074e-05 0.002043
71 RNA 3 END PROCESSING 7 98 3.285e-05 0.002153
72 CELLULAR RESPONSE TO DNA DAMAGE STIMULUS 19 720 3.529e-05 0.002281
73 MODIFICATION OF MORPHOLOGY OR PHYSIOLOGY OF OTHER ORGANISM 7 100 3.743e-05 0.002386
74 DNA TEMPLATED TRANSCRIPTION TERMINATION 7 101 3.991e-05 0.002495
75 CELLULAR MACROMOLECULAR COMPLEX ASSEMBLY 19 727 4.022e-05 0.002495
76 RNA CATABOLIC PROCESS 10 227 4.758e-05 0.002913
77 ORGANELLE FISSION 15 496 5.414e-05 0.003246
78 PROTEIN PHOSPHORYLATION 22 944 5.442e-05 0.003246
79 POSITIVE REGULATION OF MRNA METABOLIC PROCESS 5 45 5.514e-05 0.003248
80 PEPTIDYL SERINE MODIFICATION 8 148 6.678e-05 0.003884
81 REGULATION OF CELLULAR RESPONSE TO HEAT 6 76 6.95e-05 0.003944
82 MULTI ORGANISM REPRODUCTIVE PROCESS 21 891 6.933e-05 0.003944
83 POSITIVE REGULATION OF RNA SPLICING 4 25 7.382e-05 0.004089
84 POSITIVE REGULATION OF CHROMOSOME ORGANIZATION 8 150 7.34e-05 0.004089
85 MULTICELLULAR ORGANISM REPRODUCTION 19 768 8.34e-05 0.004566
86 MRNA SPLICE SITE SELECTION 4 26 8.663e-05 0.004687
87 POSITIVE REGULATION OF BIOSYNTHETIC PROCESS 33 1805 9.156e-05 0.004897
88 DNA GEOMETRIC CHANGE 6 81 9.935e-05 0.005253
89 DNA CATABOLIC PROCESS 4 27 0.000101 0.005279
90 RESPONSE TO ORGANIC CYCLIC COMPOUND 21 917 0.0001039 0.005371
91 POSITIVE REGULATION OF TELOMERASE ACTIVITY 4 28 0.000117 0.00598
92 GAMETE GENERATION 16 595 0.0001208 0.006107
93 PROTEIN IMPORT INTO NUCLEUS TRANSLOCATION 4 29 0.0001347 0.006668
94 REPRODUCTION 26 1297 0.0001342 0.006668
95 CELLULAR MACROMOLECULE LOCALIZATION 25 1234 0.0001553 0.007608
96 MALE GAMETE GENERATION 14 486 0.0001603 0.007718
97 ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS 13 427 0.0001609 0.007718
98 NEGATIVE REGULATION OF PROTEIN MODIFICATION PROCESS 16 616 0.0001793 0.008512
99 POSITIVE REGULATION OF PROTEIN LOCALIZATION TO NUCLEUS 7 129 0.0001872 0.008796
100 POSITIVE REGULATION OF MRNA PROCESSING 4 32 0.0001996 0.009281
101 VENTRICULAR CARDIAC MUSCLE CELL DEVELOPMENT 3 13 0.0002015 0.009281
102 PROTEIN STABILIZATION 7 131 0.0002058 0.00931
103 REGULATION OF PROTEIN STABILITY 9 221 0.0002061 0.00931
NumGOOverlapSizeP ValueAdj. P Value
1 RNA BINDING 87 1598 1.183e-46 1.099e-43
2 POLY A RNA BINDING 74 1170 3.639e-43 1.69e-40
3 RIBONUCLEOTIDE BINDING 64 1860 9.48e-22 2.935e-19
4 ADENYL NUCLEOTIDE BINDING 55 1514 1.564e-19 3.633e-17
5 NUCLEAR LOCALIZATION SEQUENCE BINDING 9 21 9.864e-14 1.833e-11
6 HYDROLASE ACTIVITY ACTING ON ACID ANHYDRIDES 31 820 1.699e-11 2.631e-09
7 RNA HELICASE ACTIVITY 11 67 2.291e-11 3.041e-09
8 SIGNAL SEQUENCE BINDING 9 39 6.174e-11 7.169e-09
9 PURINE NTP DEPENDENT HELICASE ACTIVITY 12 98 9.82e-11 1.014e-08
10 POLY PURINE TRACT BINDING 7 19 2.198e-10 2.042e-08
11 SINGLE STRANDED RNA BINDING 10 69 6.851e-10 5.786e-08
12 HELICASE ACTIVITY 13 153 1.612e-09 1.248e-07
13 HEAT SHOCK PROTEIN BINDING 10 89 8.75e-09 6.253e-07
14 CYCLIN DEPENDENT PROTEIN KINASE ACTIVITY 7 34 2.09e-08 1.387e-06
15 ATPASE ACTIVITY COUPLED 16 313 3.235e-08 2.003e-06
16 ATPASE ACTIVITY 18 427 8.235e-08 4.781e-06
17 PROTEIN SERINE THREONINE KINASE ACTIVITY 18 445 1.524e-07 8.328e-06
18 PROTEIN TRANSPORTER ACTIVITY 9 99 3.149e-07 1.625e-05
19 UNFOLDED PROTEIN BINDING 8 100 3.829e-06 0.0001872
20 TRANSFERASE ACTIVITY TRANSFERRING PHOSPHORUS CONTAINING GROUPS 25 992 4.223e-06 0.0001961
21 MRNA BINDING 9 155 1.318e-05 0.0005832
22 GTPASE ACTIVITY 11 246 1.728e-05 0.0007298
23 CYCLIN BINDING 4 19 2.361e-05 0.0009537
24 PROTEIN KINASE ACTIVITY 18 640 2.502e-05 0.0009684
25 DOUBLE STRANDED RNA BINDING 6 64 2.61e-05 0.0009698
26 HSP90 PROTEIN BINDING 4 27 0.000101 0.003608
27 TRANSLATION FACTOR ACTIVITY RNA BINDING 6 89 0.0001675 0.005763
28 POLY A BINDING 3 13 0.0002015 0.006601
29 AMIDE BINDING 10 272 0.000211 0.006601
30 SINGLE STRANDED DNA BINDING 6 93 0.0002132 0.006601
31 TELOMERASE RNA BINDING 3 14 0.0002547 0.007589
32 GUANYL NUCLEOTIDE BINDING 12 390 0.0002614 0.007589
33 KINASE ACTIVITY 19 842 0.0002713 0.007637
NumGOOverlapSizeP ValueAdj. P Value
1 RIBONUCLEOPROTEIN COMPLEX 46 721 4.345e-26 2.537e-23
2 CATALYTIC STEP 2 SPLICEOSOME 17 89 4.44e-18 1.296e-15
3 SPLICEOSOMAL COMPLEX 21 172 7.09e-18 1.38e-15
4 NUCLEOLUS 37 848 1.56e-15 2.277e-13
5 RIBONUCLEOPROTEIN GRANULE 14 148 8.845e-11 1.033e-08
6 NUCLEAR PORE 11 77 1.101e-10 1.071e-08
7 CYTOPLASMIC STRESS GRANULE 6 32 4.02e-07 3.354e-05
8 NUCLEAR ENVELOPE 16 416 1.493e-06 0.000109
9 NUCLEAR BODY 14 349 4.273e-06 0.0002414
10 PRP19 COMPLEX 4 13 4.547e-06 0.0002414
11 CHROMATOID BODY 4 13 4.547e-06 0.0002414
12 MICROTUBULE CYTOSKELETON 26 1068 4.962e-06 0.0002415
13 CYCLIN DEPENDENT PROTEIN KINASE HOLOENZYME COMPLEX 5 31 8.506e-06 0.0003821
14 SMALL NUCLEAR RIBONUCLEOPROTEIN COMPLEX 6 60 1.796e-05 0.0007493
15 NUCLEOPLASM PART 18 708 9.185e-05 0.003576
16 ENDOPLASMIC RETICULUM CHAPERONE COMPLEX 3 11 0.0001178 0.0043
17 PROTEIN KINASE COMPLEX 6 90 0.0001781 0.006118
18 MICROTUBULE ORGANIZING CENTER 16 623 0.0002036 0.006607
19 CYTOSKELETAL PART 27 1436 0.0002788 0.008569

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Gap_junction_hsa04540 7 88 1.628e-05 0.0004888
2 Cell_cycle_hsa04110 8 124 1.88e-05 0.0004888
3 Cellular_senescence_hsa04218 8 160 0.0001152 0.001904
4 Oocyte_meiosis_hsa04114 7 124 0.0001464 0.001904
5 p53_signaling_pathway_hsa04115 4 68 0.003501 0.03642
6 Adherens_junction_hsa04520 4 72 0.0043 0.03727
7 FoxO_signaling_pathway_hsa04068 5 132 0.007378 0.05481
8 Apoptosis_hsa04210 5 138 0.008852 0.05754
9 Phagosome_hsa04145 5 152 0.01306 0.07543
10 Tight_junction_hsa04530 5 170 0.02021 0.1051
11 Hippo_signaling_pathway_multiple_species_hsa04392 2 29 0.02876 0.1359
12 Wnt_signaling_pathway_hsa04310 4 146 0.04533 0.1964
13 Hippo_signaling_pathway_hsa04390 4 154 0.05322 0.2129
14 VEGF_signaling_pathway_hsa04370 2 59 0.1016 0.3641
15 PI3K_Akt_signaling_pathway_hsa04151 6 352 0.105 0.3641
16 MAPK_signaling_pathway_hsa04010 5 295 0.1346 0.4376
17 mTOR_signaling_pathway_hsa04150 3 151 0.1608 0.4919
18 TGF_beta_signaling_pathway_hsa04350 2 84 0.1794 0.5142
19 cGMP_PKG_signaling_pathway_hsa04022 3 163 0.1879 0.5142
20 NF_kappa_B_signaling_pathway_hsa04064 2 95 0.2159 0.5614
21 HIF_1_signaling_pathway_hsa04066 2 100 0.2328 0.5764
22 Regulation_of_actin_cytoskeleton_hsa04810 3 208 0.2969 0.6962
23 Calcium_signaling_pathway_hsa04020 2 182 0.4978 0.9588
24 Focal_adhesion_hsa04510 2 199 0.5457 0.9783
25 Rap1_signaling_pathway_hsa04015 2 206 0.5644 0.9783
26 Endocytosis_hsa04144 2 244 0.6565 1

Quest ID: 06ce305054faac37997f368a7a28c132