Visible node/edge number:
Node colors:
Node labels:

show label of nodes with degree >=

Node sizes:
Edge colors:
Edge widths factor:
Layout:

gravity >=

edgeLength =

GRN in network:

Notice: IE browser need to manually refresh (F5) this page after resetting the network.

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-101-3p SOX9 -1.48 0 0.46 0.17811 miRNAWalker2 validate; miRNATAP -0.92 0 23178713 Ectopic expression of miR-101 significantly inhibited HCC cell proliferation and tumorigenicity by targeting SOX9; Therefore miR-101 may suppress HCC tumor progression by down-regulating SOX9
2 hsa-miR-30e-5p SOX9 -0.63 0 0.46 0.17811 MirTarget -0.79 0 NA
3 hsa-miR-616-5p SOX9 0.15 0.40284 0.46 0.17811 mirMAP; miRNATAP -0.34 0.0002 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 CELLULAR RESPONSE TO ENDOGENOUS STIMULUS 21 1008 1.734e-13 8.067e-10
2 RESPONSE TO OXYGEN CONTAINING COMPOUND 23 1381 9.078e-13 2.112e-09
3 CELLULAR RESPONSE TO HORMONE STIMULUS 16 552 1.861e-12 2.886e-09
4 RESPONSE TO ENDOGENOUS STIMULUS 23 1450 2.493e-12 2.9e-09
5 CELLULAR RESPONSE TO ORGANIC SUBSTANCE 25 1848 6.312e-12 5.874e-09
6 RESPONSE TO HORMONE 18 893 2.515e-11 1.95e-08
7 RESPONSE TO LIPID 17 888 2.279e-10 1.515e-07
8 RESPONSE TO NITROGEN COMPOUND 16 859 1.294e-09 7.525e-07
9 CELLULAR RESPONSE TO OXYGEN CONTAINING COMPOUND 15 799 4.259e-09 2.202e-06
10 CELLULAR RESPONSE TO LIPID 12 457 4.89e-09 2.276e-06
11 REGULATION OF HORMONE LEVELS 12 478 8.073e-09 3.415e-06
12 POSITIVE REGULATION OF GLUCOSE METABOLIC PROCESS 5 36 5.537e-08 2.147e-05
13 CELLULAR RESPONSE TO ORGANIC CYCLIC COMPOUND 11 465 6.712e-08 2.342e-05
14 REGULATION OF CELL DEATH 18 1472 7.048e-08 2.342e-05
15 LIPID METABOLIC PROCESS 16 1158 8.748e-08 2.714e-05
16 DEVELOPMENTAL PROCESS INVOLVED IN REPRODUCTION 12 602 1.018e-07 2.959e-05
17 RESPONSE TO PEPTIDE 10 404 1.875e-07 4.846e-05
18 CELLULAR RESPONSE TO STEROID HORMONE STIMULUS 8 218 1.83e-07 4.846e-05
19 RESPONSE TO ORGANIC CYCLIC COMPOUND 14 917 2.004e-07 4.907e-05
20 RESPONSE TO ACID CHEMICAL 9 319 2.741e-07 6.378e-05
21 REGULATION OF PHOSPHORUS METABOLIC PROCESS 18 1618 2.926e-07 6.482e-05
22 STEROID METABOLIC PROCESS 8 237 3.462e-07 7.321e-05
23 REPRODUCTION 16 1297 4.093e-07 7.963e-05
24 HORMONE METABOLIC PROCESS 7 164 4.107e-07 7.963e-05
25 CELLULAR HORMONE METABOLIC PROCESS 6 104 5.003e-07 9.311e-05
26 SEX DIFFERENTIATION 8 266 8.289e-07 0.0001483
27 RESPONSE TO LITHIUM ION 4 27 9.906e-07 0.0001707
28 OXIDATION REDUCTION PROCESS 13 898 1.079e-06 0.0001793
29 RESPONSE TO STEROID HORMONE 10 497 1.243e-06 0.0001994
30 POSITIVE REGULATION OF BIOSYNTHETIC PROCESS 18 1805 1.459e-06 0.0002189
31 CELLULAR RESPONSE TO NITROGEN COMPOUND 10 505 1.435e-06 0.0002189
32 ANDROGEN METABOLIC PROCESS 4 30 1.537e-06 0.0002235
33 GLAND DEVELOPMENT 9 395 1.625e-06 0.0002291
34 RESPONSE TO INSULIN 7 205 1.838e-06 0.0002515
35 REPRODUCTIVE SYSTEM DEVELOPMENT 9 408 2.12e-06 0.000274
36 ORGANIC ACID METABOLIC PROCESS 13 953 2.091e-06 0.000274
37 POSITIVE REGULATION OF CARBOHYDRATE METABOLIC PROCESS 5 75 2.33e-06 0.000293
38 DEVELOPMENT OF PRIMARY SEXUAL CHARACTERISTICS 7 216 2.6e-06 0.0003184
39 CELLULAR RESPONSE TO INSULIN STIMULUS 6 146 3.646e-06 0.000435
40 TRANSCRIPTION INITIATION FROM RNA POLYMERASE II PROMOTER 6 153 4.778e-06 0.0005515
41 REGULATION OF CARBOHYDRATE BIOSYNTHETIC PROCESS 5 87 4.859e-06 0.0005515
42 HORMONE MEDIATED SIGNALING PATHWAY 6 158 5.75e-06 0.0006337
43 SYSTEM PROCESS 17 1785 5.857e-06 0.0006337
44 CELL DEVELOPMENT 15 1426 7.377e-06 0.0007802
45 ANDROGEN BIOSYNTHETIC PROCESS 3 14 7.813e-06 0.0008079
46 MULTICELLULAR ORGANISM REPRODUCTION 11 768 9.15e-06 0.0009255
47 REGULATION OF GLUCOSE TRANSPORT 5 100 9.626e-06 0.0009331
48 CELLULAR RESPONSE TO ABIOTIC STIMULUS 7 263 9.471e-06 0.0009331
49 CELLULAR RESPONSE TO PEPTIDE 7 274 1.236e-05 0.001173
50 REGULATION OF GLUCOSE METABOLIC PROCESS 5 106 1.279e-05 0.00119
51 REGULATION OF CELL PROLIFERATION 15 1496 1.313e-05 0.001198
52 CELLULAR RESPONSE TO LITHIUM ION 3 17 1.451e-05 0.001274
53 POSITIVE REGULATION OF GLYCOGEN METABOLIC PROCESS 3 17 1.451e-05 0.001274
54 RESPONSE TO AMINO ACID 5 112 1.671e-05 0.00144
55 NOTCH SIGNALING PATHWAY 5 114 1.821e-05 0.001541
56 LIPID BIOSYNTHETIC PROCESS 9 539 1.995e-05 0.001657
57 POSITIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 12 1004 2.089e-05 0.001705
58 DNA TEMPLATED TRANSCRIPTION INITIATION 6 202 2.329e-05 0.001869
59 REGULATION OF GLUCOSE IMPORT 4 60 2.567e-05 0.00199
60 RESPONSE TO ABIOTIC STIMULUS 12 1024 2.538e-05 0.00199
61 POSITIVE REGULATION OF PHOSPHATE METABOLIC PROCESS 12 1036 2.847e-05 0.002045
62 RESPONSE TO OXYGEN LEVELS 7 311 2.791e-05 0.002045
63 POSITIVE REGULATION OF PHOSPHORUS METABOLIC PROCESS 12 1036 2.847e-05 0.002045
64 RESPONSE TO DRUG 8 431 2.857e-05 0.002045
65 STEROID HORMONE MEDIATED SIGNALING PATHWAY 5 125 2.841e-05 0.002045
66 NEGATIVE REGULATION OF CELL DEATH 11 872 2.98e-05 0.002101
67 HEPATICOBILIARY SYSTEM DEVELOPMENT 5 128 3.184e-05 0.002211
68 RESPONSE TO IMMOBILIZATION STRESS 3 22 3.252e-05 0.002226
69 REGULATION OF REPRODUCTIVE PROCESS 5 129 3.305e-05 0.002229
70 RESPONSE TO EXTRACELLULAR STIMULUS 8 441 3.363e-05 0.002235
71 REGULATION OF MULTICELLULAR ORGANISMAL DEVELOPMENT 15 1672 4.852e-05 0.003179
72 POSITIVE REGULATION OF CELL DEATH 9 605 4.919e-05 0.003179
73 RESPONSE TO INORGANIC SUBSTANCE 8 479 6.024e-05 0.00384
74 EPITHELIUM DEVELOPMENT 11 945 6.19e-05 0.003892
75 MUSCLE HYPERTROPHY 3 28 6.835e-05 0.004191
76 TISSUE DEVELOPMENT 14 1518 6.845e-05 0.004191
77 HOMEOSTATIC PROCESS 13 1337 7.713e-05 0.004661
78 NEGATIVE REGULATION OF CELL PROLIFERATION 9 643 7.858e-05 0.004688
79 REGULATION OF NEURON DEATH 6 252 7.99e-05 0.004706
80 MONOCARBOXYLIC ACID METABOLIC PROCESS 8 503 8.474e-05 0.004868
81 BROWN FAT CELL DIFFERENTIATION 3 30 8.437e-05 0.004868
82 SMALL MOLECULE METABOLIC PROCESS 15 1767 9.133e-05 0.005182
83 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 15 1784 0.0001018 0.005706
84 INTRACELLULAR RECEPTOR SIGNALING PATHWAY 5 168 0.0001159 0.006421
85 REGULATION OF GENERATION OF PRECURSOR METABOLITES AND ENERGY 4 89 0.0001209 0.006616
86 REGULATION OF CARBOHYDRATE METABOLIC PROCESS 5 172 0.0001294 0.007003
87 REGULATION OF GLYCOGEN METABOLIC PROCESS 3 35 0.0001346 0.007201
88 REGULATION OF NUCLEOTIDE CATABOLIC PROCESS 3 36 0.0001466 0.007646
89 REGULATION OF LIPID METABOLIC PROCESS 6 282 0.0001479 0.007646
90 REGULATION OF TRANSCRIPTION REGULATORY REGION DNA BINDING 3 36 0.0001466 0.007646
91 REGULATION OF GLUCONEOGENESIS 3 38 0.0001725 0.00882
92 DRUG METABOLIC PROCESS 3 39 0.0001865 0.009418
93 MULTI ORGANISM REPRODUCTIVE PROCESS 10 891 0.0001882 0.009418
94 TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 9 724 0.0001926 0.009534
95 DICARBOXYLIC ACID METABOLIC PROCESS 4 101 0.0001971 0.009652
96 RHYTHMIC PROCESS 6 298 0.0001994 0.009667
97 UROGENITAL SYSTEM DEVELOPMENT 6 299 0.0002031 0.009742
NumGOOverlapSizeP ValueAdj. P Value
1 OXYGEN BINDING 5 47 2.2e-07 0.0002044
2 STEROID HORMONE RECEPTOR ACTIVITY 5 59 6.996e-07 0.0002166
3 OXIDOREDUCTASE ACTIVITY 12 719 6.808e-07 0.0002166
4 RNA POLYMERASE II TRANSCRIPTION FACTOR ACTIVITY SEQUENCE SPECIFIC DNA BINDING 11 629 1.351e-06 0.0002511
5 DOUBLE STRANDED DNA BINDING 12 764 1.289e-06 0.0002511
6 STEROID HYDROXYLASE ACTIVITY 4 31 1.761e-06 0.0002727
7 REGULATORY REGION NUCLEIC ACID BINDING 12 818 2.621e-06 0.00034
8 TRANSCRIPTIONAL ACTIVATOR ACTIVITY RNA POLYMERASE II TRANSCRIPTION REGULATORY REGION SEQUENCE SPECIFIC BINDING 8 315 2.928e-06 0.00034
9 TRANSCRIPTIONAL ACTIVATOR ACTIVITY RNA POLYMERASE II CORE PROMOTER PROXIMAL REGION SEQUENCE SPECIFIC BINDING 7 226 3.507e-06 0.000362
10 TRANSCRIPTION FACTOR ACTIVITY RNA POLYMERASE II CORE PROMOTER PROXIMAL REGION SEQUENCE SPECIFIC BINDING 8 328 3.947e-06 0.0003666
11 STEROID BINDING 5 91 6.063e-06 0.0004694
12 MACROMOLECULAR COMPLEX BINDING 15 1399 5.85e-06 0.0004694
13 INSULIN LIKE GROWTH FACTOR RECEPTOR BINDING 3 15 9.747e-06 0.0006965
14 TRANSCRIPTION FACTOR ACTIVITY DIRECT LIGAND REGULATED SEQUENCE SPECIFIC DNA BINDING 4 48 1.051e-05 0.0006971
15 TRANSCRIPTION FACTOR BINDING 9 524 1.596e-05 0.0009883
16 ENZYME BINDING 16 1737 1.819e-05 0.001056
17 HORMONE BINDING 4 65 3.526e-05 0.001927
18 TETRAPYRROLE BINDING 5 134 3.966e-05 0.002047
19 PROTEIN COMPLEX BINDING 11 935 5.624e-05 0.00275
20 IRON ION BINDING 5 163 0.0001006 0.004671
21 SEQUENCE SPECIFIC DNA BINDING 11 1037 0.0001416 0.006263
22 MONOOXYGENASE ACTIVITY 4 95 0.0001556 0.006571
23 PROTEIN HOMODIMERIZATION ACTIVITY 9 722 0.0001887 0.007621
24 RNA POLYMERASE II TRANSCRIPTION FACTOR BINDING 4 104 0.0002205 0.008536
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 hsa04510_Focal_adhesion 7 200 1.559e-06 0.0002759
2 hsa00140_Steroid_hormone_biosynthesis 4 57 2.092e-05 0.001852
3 hsa04910_Insulin_signaling_pathway 5 138 4.565e-05 0.002693
4 hsa04512_ECM.receptor_interaction 4 85 0.0001011 0.004473
5 hsa04960_Aldosterone.regulated_sodium_reabsorption 3 42 0.0002328 0.008243
6 hsa00830_Retinol_metabolism 3 64 0.0008084 0.02064
7 hsa04920_Adipocytokine_signaling_pathway 3 68 0.0009645 0.02064
8 hsa04115_p53_signaling_pathway 3 69 0.001006 0.02064
9 hsa03320_PPAR_signaling_pathway 3 70 0.001049 0.02064
10 hsa00020_Citrate_cycle_.TCA_cycle. 2 30 0.003298 0.05838
11 hsa04650_Natural_killer_cell_mediated_cytotoxicity 3 136 0.006885 0.1108
12 hsa04150_mTOR_signaling_pathway 2 52 0.009658 0.1414
13 hsa00500_Starch_and_sucrose_metabolism 2 54 0.01039 0.1414
14 hsa00980_Metabolism_of_xenobiotics_by_cytochrome_P450 2 71 0.01749 0.2101
15 hsa04662_B_cell_receptor_signaling_pathway 2 75 0.01939 0.2101
16 hsa04370_VEGF_signaling_pathway 2 76 0.01988 0.2101
17 hsa04070_Phosphatidylinositol_signaling_system 2 78 0.02087 0.2101
18 hsa04664_Fc_epsilon_RI_signaling_pathway 2 79 0.02137 0.2101
19 hsa04810_Regulation_of_actin_cytoskeleton 3 214 0.02315 0.2146
20 hsa04012_ErbB_signaling_pathway 2 87 0.02558 0.2146
21 hsa04914_Progesterone.mediated_oocyte_maturation 2 87 0.02558 0.2146
22 hsa04210_Apoptosis 2 89 0.02668 0.2146
23 hsa04010_MAPK_signaling_pathway 3 268 0.04098 0.3093
24 hsa04114_Oocyte_meiosis 2 114 0.04195 0.3093
25 hsa04722_Neurotrophin_signaling_pathway 2 127 0.0509 0.3263
26 hsa04110_Cell_cycle 2 128 0.05162 0.3263
27 hsa00190_Oxidative_phosphorylation 2 132 0.05452 0.3328
28 hsa04310_Wnt_signaling_pathway 2 151 0.06903 0.3941

Quest ID: b66396e86ed4800de5f6e55bff51d619