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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-107 ACTG2 1.31 0 -5.39 0 miRanda -1.98 0 NA
2 hsa-miR-125a-5p ACTG2 0.6 0.01023 -5.39 0 miRanda -0.51 0.00044 NA
3 hsa-miR-129-5p ACTG2 -0.52 0.22258 -5.39 0 miRanda -0.33 3.0E-5 NA
4 hsa-miR-193a-3p ACTG2 1.6 0 -5.39 0 miRanda -0.29 0.00696 NA
5 hsa-miR-590-3p ACTG2 2.59 0 -5.39 0 miRanda -1.27 0 NA
6 hsa-miR-107 MYH11 1.31 0 -6.47 0 miRanda -2.04 0 NA
7 hsa-miR-129-5p MYH11 -0.52 0.22258 -6.47 0 miRanda -0.36 3.0E-5 NA
8 hsa-miR-146b-5p MYH11 1.76 0 -6.47 0 miRanda -0.22 0.04348 NA
9 hsa-miR-193a-3p MYH11 1.6 0 -6.47 0 PITA; miRanda -0.59 0 NA
10 hsa-miR-19a-3p MYH11 3.42 0 -6.47 0 MirTarget -1.32 0 NA
11 hsa-miR-19b-3p MYH11 2.5 0 -6.47 0 MirTarget -1.73 0 NA
12 hsa-miR-342-5p MYH11 1.75 0 -6.47 0 miRNATAP -1.11 0 NA
13 hsa-miR-34c-5p MYH11 2.07 0 -6.47 0 miRanda -0.46 0 NA
14 hsa-miR-3614-5p MYH11 2.18 0 -6.47 0 miRNATAP -0.71 0 NA
15 hsa-miR-421 MYH11 1.18 1.0E-5 -6.47 0 miRanda -0.98 0 NA
16 hsa-miR-491-5p MYH11 0.62 0.04183 -6.47 0 miRanda -0.83 0 NA
17 hsa-miR-590-5p MYH11 3.18 0 -6.47 0 miRanda -1.49 0 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 CHROMOSOME ORGANIZATION 55 1009 1.852e-16 8.618e-13
2 MITOTIC CELL CYCLE 46 766 2.184e-15 5.081e-12
3 CELL CYCLE PROCESS 54 1081 1.401e-14 2.174e-11
4 CELL CYCLE 60 1316 2.212e-14 2.573e-11
5 MITOTIC NUCLEAR DIVISION 30 361 6.369e-14 5.927e-11
6 ORGANELLE FISSION 34 496 3.346e-13 2.595e-10
7 MICROTUBULE BASED PROCESS 34 522 1.414e-12 9.397e-10
8 CELL DIVISION 30 460 3.089e-11 1.797e-08
9 MITOTIC SISTER CHROMATID SEGREGATION 14 91 1.158e-10 5.987e-08
10 MICROTUBULE CYTOSKELETON ORGANIZATION 25 348 1.964e-10 9.14e-08
11 CHROMATIN MODIFICATION 31 539 3.288e-10 1.391e-07
12 CHROMATIN REMODELING 16 150 1.452e-09 5.63e-07
13 REGULATION OF ORGANELLE ORGANIZATION 47 1178 1.862e-09 6.189e-07
14 NEGATIVE REGULATION OF ORGANELLE ORGANIZATION 25 387 1.786e-09 6.189e-07
15 MICROTUBULE BASED MOVEMENT 18 205 3.201e-09 9.93e-07
16 REGULATION OF MICROTUBULE BASED PROCESS 19 243 7.961e-09 2.315e-06
17 NEGATIVE REGULATION OF CYTOSKELETON ORGANIZATION 18 221 1.05e-08 2.875e-06
18 CHROMATIN ORGANIZATION 32 663 1.223e-08 3.162e-06
19 DNA METABOLIC PROCESS 34 758 2.538e-08 6.215e-06
20 REGULATION OF CYTOSKELETON ORGANIZATION 26 502 7.772e-08 1.808e-05
21 CELL CYCLE PHASE TRANSITION 18 255 9.5e-08 2.103e-05
22 SISTER CHROMATID SEGREGATION 15 176 9.945e-08 2.103e-05
23 ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE OR POLYSACCHARIDE ANTIGEN VIA MHC CLASS II 11 94 2.145e-07 4.026e-05
24 ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE ANTIGEN VIA MHC CLASS II 11 94 2.145e-07 4.026e-05
25 METAPHASE PLATE CONGRESSION 8 42 2.163e-07 4.026e-05
26 CHROMOSOME SEGREGATION 18 272 2.495e-07 4.465e-05
27 RETROGRADE VESICLE MEDIATED TRANSPORT GOLGI TO ER 10 77 2.859e-07 4.761e-05
28 NEGATIVE REGULATION OF CELLULAR COMPONENT ORGANIZATION 30 684 2.865e-07 4.761e-05
29 PROTEIN COMPLEX SUBUNIT ORGANIZATION 49 1527 7.287e-07 0.0001169
30 MITOTIC SPINDLE ORGANIZATION 9 69 1.093e-06 0.0001695
31 DNA REPAIR 23 480 1.707e-06 0.0002562
32 COVALENT CHROMATIN MODIFICATION 19 345 1.878e-06 0.0002731
33 PROTEIN COMPLEX BIOGENESIS 39 1132 2.137e-06 0.0002924
34 PROTEIN COMPLEX ASSEMBLY 39 1132 2.137e-06 0.0002924
35 NEGATIVE REGULATION OF PROTEIN COMPLEX DISASSEMBLY 13 170 2.435e-06 0.0003238
36 MITOTIC SPINDLE ASSEMBLY 7 41 2.753e-06 0.0003371
37 MICROTUBULE CYTOSKELETON ORGANIZATION INVOLVED IN MITOSIS 7 41 2.753e-06 0.0003371
38 NUCLEAR CHROMOSOME SEGREGATION 15 228 2.72e-06 0.0003371
39 REGULATION OF MICROTUBULE POLYMERIZATION OR DEPOLYMERIZATION 13 178 4.055e-06 0.0004838
40 CHROMOSOME LOCALIZATION 8 61 4.188e-06 0.0004872
41 MACROMOLECULAR COMPLEX ASSEMBLY 44 1398 4.786e-06 0.0005432
42 DNA CONFORMATION CHANGE 16 273 5.627e-06 0.0006234
43 CYTOSKELETON ORGANIZATION 31 838 6.371e-06 0.0006894
44 REGULATION OF PROTEIN COMPLEX DISASSEMBLY 14 217 7.33e-06 0.0007579
45 CELLULAR RESPONSE TO DNA DAMAGE STIMULUS 28 720 7.316e-06 0.0007579
46 SPINDLE ASSEMBLY 8 70 1.191e-05 0.001205
47 REGULATION OF MITOTIC CELL CYCLE 21 468 1.32e-05 0.001307
48 NEGATIVE REGULATION OF MITOTIC CELL CYCLE 13 199 1.36e-05 0.001318
49 ATP DEPENDENT CHROMATIN REMODELING 8 74 1.803e-05 0.001712
50 REGULATION OF CELL DIVISION 15 272 2.262e-05 0.002105
51 CYTOSKELETON DEPENDENT CYTOKINESIS 6 39 2.702e-05 0.002465
52 REGULATION OF CELL CYCLE 32 949 2.859e-05 0.002559
53 POSITIVE REGULATION OF CELL CYCLE PROCESS 14 247 3.137e-05 0.002754
54 MICROTUBULE DEPOLYMERIZATION 4 13 3.534e-05 0.00299
55 DNA GEOMETRIC CHANGE 8 81 3.505e-05 0.00299
56 PEPTIDYL AMINO ACID MODIFICATION 29 841 4.637e-05 0.003853
57 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 49 1784 4.958e-05 0.004048
58 CELL CYCLE G1 S PHASE TRANSITION 9 111 5.541e-05 0.00437
59 G1 S TRANSITION OF MITOTIC CELL CYCLE 9 111 5.541e-05 0.00437
60 CELL CYCLE G2 M PHASE TRANSITION 10 138 5.642e-05 0.004376
61 REGULATION OF CELL CYCLE PROCESS 22 558 5.859e-05 0.004469
62 MITOTIC CELL CYCLE CHECKPOINT 10 139 5.998e-05 0.004502
63 HISTONE H2A ACETYLATION 4 15 6.585e-05 0.004863
64 CELLULAR RESPONSE TO STRESS 44 1565 7.421e-05 0.005395
65 ORGANELLE LOCALIZATION 18 415 8.47e-05 0.006063
66 CENTROMERE COMPLEX ASSEMBLY 6 48 9.048e-05 0.006379
67 ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE ANTIGEN 11 177 9.79e-05 0.006799
68 MITOTIC CYTOKINESIS 5 31 0.0001026 0.006817
69 PEPTIDYL SERINE MODIFICATION 10 148 0.0001016 0.006817
70 MISMATCH REPAIR 5 31 0.0001026 0.006817
71 HISTONE H4 ACETYLATION 6 50 0.0001142 0.007483
72 DNA RECOMBINATION 12 215 0.0001328 0.008579
73 GOLGI VESICLE TRANSPORT 15 319 0.0001373 0.008752
74 SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR 9 127 0.0001569 0.009732
75 CELLULAR COMPONENT DISASSEMBLY 20 515 0.0001554 0.009732
NumGOOverlapSizeP ValueAdj. P Value
1 RIBONUCLEOTIDE BINDING 78 1860 1.089e-16 7.23e-14
2 ADENYL NUCLEOTIDE BINDING 69 1514 1.557e-16 7.23e-14
3 MICROTUBULE MOTOR ACTIVITY 17 77 2.115e-15 6.549e-13
4 NUCLEIC ACID BINDING TRANSCRIPTION FACTOR ACTIVITY 58 1199 5.062e-15 1.176e-12
5 MACROMOLECULAR COMPLEX BINDING 61 1399 9.366e-14 1.74e-11
6 HYDROLASE ACTIVITY ACTING ON ACID ANHYDRIDES 45 820 1.151e-13 1.782e-11
7 MOTOR ACTIVITY 19 131 1.565e-13 2.077e-11
8 ATPASE ACTIVITY 31 427 8.832e-13 1.026e-10
9 DOUBLE STRANDED DNA BINDING 41 764 3.273e-12 3.379e-10
10 MICROTUBULE BINDING 20 201 4.428e-11 4.113e-09
11 SEQUENCE SPECIFIC DNA BINDING 46 1037 9.363e-11 7.907e-09
12 TUBULIN BINDING 22 273 2.868e-10 2.221e-08
13 PROTEIN COMPLEX BINDING 42 935 4.647e-10 3.321e-08
14 CORE PROMOTER PROXIMAL REGION DNA BINDING 25 371 7.487e-10 4.968e-08
15 ATP DEPENDENT MICROTUBULE MOTOR ACTIVITY 7 18 5.281e-09 3.271e-07
16 CHROMATIN BINDING 24 435 7.822e-08 4.541e-06
17 CYTOSKELETAL PROTEIN BINDING 34 819 1.612e-07 8.809e-06
18 REGULATORY REGION NUCLEIC ACID BINDING 33 818 4.74e-07 2.446e-05
19 STRUCTURE SPECIFIC DNA BINDING 11 118 2.143e-06 0.0001048
20 HELICASE ACTIVITY 12 153 4.581e-06 0.0002128
21 DAMAGED DNA BINDING 8 63 5.363e-06 0.0002333
22 NUCLEOSOMAL DNA BINDING 6 30 5.525e-06 0.0002333
23 DNA HELICASE ACTIVITY 7 53 1.612e-05 0.0006511
24 HISTONE BINDING 12 177 2.017e-05 0.0007806
25 MISMATCHED DNA BINDING 4 12 2.477e-05 0.0009204
26 NUCLEOSOME BINDING 6 45 6.242e-05 0.002148
27 RNA POLYMERASE II DISTAL ENHANCER SEQUENCE SPECIFIC DNA BINDING 7 65 6.218e-05 0.002148
28 PROTEIN SERINE THREONINE KINASE ACTIVITY 19 445 6.65e-05 0.002206
29 ENHANCER BINDING 8 93 9.463e-05 0.003031
30 PROTEIN KINASE ACTIVITY 23 640 0.0001589 0.004919
31 DNA DEPENDENT ATPASE ACTIVITY 7 79 0.0002155 0.006459
32 CHROMATIN DNA BINDING 7 80 0.0002331 0.006768
33 TRANSFERASE ACTIVITY TRANSFERRING PHOSPHORUS CONTAINING GROUPS 30 992 0.0003429 0.009653
NumGOOverlapSizeP ValueAdj. P Value
1 KINESIN COMPLEX 18 55 1.244e-19 7.266e-17
2 MICROTUBULE CYTOSKELETON 52 1068 1.282e-13 2.496e-11
3 MICROTUBULE ASSOCIATED COMPLEX 20 145 9.43e-14 2.496e-11
4 CYTOSKELETAL PART 56 1436 9.355e-11 1.366e-08
5 NUCLEAR CHROMOSOME 31 523 1.566e-10 1.829e-08
6 CHROMOSOME 41 880 2.586e-10 2.517e-08
7 SWI SNF SUPERFAMILY TYPE COMPLEX 12 71 8.175e-10 6.171e-08
8 SPINDLE 22 289 8.453e-10 6.171e-08
9 MICROTUBULE 26 405 9.522e-10 6.179e-08
10 MICROTUBULE ORGANIZING CENTER 32 623 2.756e-09 1.609e-07
11 CYTOSKELETON 62 1967 3.4e-08 1.805e-06
12 CENTROSOME 26 487 4.258e-08 2.072e-06
13 MITOTIC SPINDLE 9 55 1.481e-07 6.651e-06
14 SUPRAMOLECULAR FIBER 30 670 1.844e-07 7.693e-06
15 MIDBODY 12 132 9.655e-07 3.759e-05
16 NUCLEOPLASM PART 29 708 1.812e-06 6.615e-05
17 TRANSFERASE COMPLEX 28 703 4.681e-06 0.0001608
18 CHROMATIN 21 441 5.358e-06 0.0001738
19 NUCLEAR CHROMATIN 16 291 1.254e-05 0.0003855
20 CONDENSED CHROMOSOME OUTER KINETOCHORE 4 12 2.477e-05 0.0006888
21 ACETYLTRANSFERASE COMPLEX 9 100 2.418e-05 0.0006888
22 SPINDLE MICROTUBULE 7 58 2.944e-05 0.0007815
23 SPINDLE MIDZONE 5 27 5.125e-05 0.001301
24 NUCLEOLUS 29 848 5.373e-05 0.001307
25 CHROMOSOMAL REGION 16 330 5.764e-05 0.001346
26 TRANSFERASE COMPLEX TRANSFERRING PHOSPHORUS CONTAINING GROUPS 13 237 8.37e-05 0.00188
27 RNA POLYMERASE COMPLEX 9 122 0.0001154 0.002324
28 CHD TYPE COMPLEX 4 17 0.000112 0.002324
29 NUCLEAR PERIPHERY 9 121 0.0001084 0.002324
30 CATALYTIC COMPLEX 32 1038 0.0001535 0.002988
31 H4 HISTONE ACETYLTRANSFERASE COMPLEX 4 19 0.0001781 0.003355
32 INO80 TYPE COMPLEX 4 21 0.0002684 0.004898
33 NUCLEAR REPLICATION FORK 5 39 0.0003142 0.005561
34 NUCLEAR TRANSCRIPTIONAL REPRESSOR COMPLEX 4 22 0.0003241 0.005567
35 BAF TYPE COMPLEX 4 23 0.0003876 0.006467
36 METHYLTRANSFERASE COMPLEX 7 90 0.0004811 0.007805

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Cell_cycle_hsa04110 13 124 6.326e-08 3.29e-06
2 Oocyte_meiosis_hsa04114 8 124 0.0006788 0.01765
3 Cellular_senescence_hsa04218 8 160 0.003424 0.05148
4 p53_signaling_pathway_hsa04115 5 68 0.00396 0.05148
5 Tight_junction_hsa04530 7 170 0.01645 0.1435
6 FoxO_signaling_pathway_hsa04068 6 132 0.01655 0.1435
7 Notch_signaling_pathway_hsa04330 3 48 0.03761 0.2794
8 Gap_junction_hsa04540 4 88 0.04705 0.3058
9 VEGF_signaling_pathway_hsa04370 3 59 0.06259 0.3578
10 HIF_1_signaling_pathway_hsa04066 4 100 0.0688 0.3578
11 Hippo_signaling_pathway_hsa04390 5 154 0.09 0.4255
12 Hedgehog_signaling_pathway_hsa04340 2 47 0.1632 0.6211
13 Apoptosis_hsa04210 4 138 0.1642 0.6211
14 Signaling_pathways_regulating_pluripotency_of_stem_cells_hsa04550 4 139 0.1672 0.6211
15 Sphingolipid_signaling_pathway_hsa04071 3 118 0.2734 0.9479
16 Adherens_junction_hsa04520 2 72 0.3046 0.9702
17 Endocytosis_hsa04144 5 244 0.3232 0.9702
18 Peroxisome_hsa04146 2 83 0.3664 0.9702
19 TGF_beta_signaling_pathway_hsa04350 2 84 0.3719 0.9702
20 Phospholipase_D_signaling_pathway_hsa04072 3 146 0.391 0.9702
21 Rap1_signaling_pathway_hsa04015 4 206 0.3918 0.9702
22 PI3K_Akt_signaling_pathway_hsa04151 6 352 0.4586 1
23 cGMP_PKG_signaling_pathway_hsa04022 3 163 0.4603 1
24 Calcium_signaling_pathway_hsa04020 3 182 0.5336 1
25 Focal_adhesion_hsa04510 3 199 0.5941 1
26 Regulation_of_actin_cytoskeleton_hsa04810 3 208 0.624 1
27 Apelin_signaling_pathway_hsa04371 2 137 0.6261 1
28 Wnt_signaling_pathway_hsa04310 2 146 0.6605 1
29 MAPK_signaling_pathway_hsa04010 4 295 0.6688 1
30 mTOR_signaling_pathway_hsa04150 2 151 0.6784 1
31 Necroptosis_hsa04217 2 164 0.7216 1
32 Ras_signaling_pathway_hsa04014 2 232 0.8751 1
33 Neuroactive_ligand_receptor_interaction_hsa04080 2 278 0.9298 1

lncRNA-mediated sponge

(Download full result)

Num lncRNA miRNAs           miRNAs count     Gene Sponge regulatory network lncRNA log2FC lncRNA pvalue Gene log2FC Gene pvalue lncRNA-gene Pearson correlation
1 MIR143HG hsa-miR-107;hsa-miR-129-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-342-5p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-491-5p;hsa-miR-590-5p 10 MYH11 Sponge network -4.237 0 -6.469 0 0.835
2 HAND2-AS1 hsa-miR-107;hsa-miR-129-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-342-5p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-421;hsa-miR-491-5p 10 MYH11 Sponge network -5.605 0 -6.469 0 0.764
3 ADAMTS9-AS1 hsa-miR-107;hsa-miR-129-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-421;hsa-miR-491-5p;hsa-miR-590-5p 10 MYH11 Sponge network -7.614 0 -6.469 0 0.761
4 FENDRR hsa-miR-107;hsa-miR-129-5p;hsa-miR-146b-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-342-5p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-421 10 MYH11 Sponge network -4.793 0 -6.469 0 0.745
5 RP11-887P2.5 hsa-miR-107;hsa-miR-129-5p;hsa-miR-146b-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-421;hsa-miR-590-5p 10 MYH11 Sponge network -6.751 0 -6.469 0 0.662
6 PART1 hsa-miR-107;hsa-miR-129-5p;hsa-miR-146b-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-342-5p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-491-5p;hsa-miR-590-5p 11 MYH11 Sponge network -3.06 7.0E-5 -6.469 0 0.376
7 SNHG14 hsa-miR-107;hsa-miR-146b-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-342-5p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-421;hsa-miR-590-5p 10 MYH11 Sponge network -2.055 0 -6.469 0 0.351
8 TPTEP1 hsa-miR-107;hsa-miR-146b-5p;hsa-miR-193a-3p;hsa-miR-19a-3p;hsa-miR-19b-3p;hsa-miR-342-5p;hsa-miR-34c-5p;hsa-miR-3614-5p;hsa-miR-421;hsa-miR-590-5p 10 MYH11 Sponge network -2.267 2.0E-5 -6.469 0 0.279

Quest ID: fd34271f561b43e865b7379ffb32f944