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-107 SGK1 0.24 0.01708 -1.42 0 miRanda -0.32 0.00197 NA
2 hsa-miR-15b-5p SGK1 0.23 0.08248 -1.42 0 miRNATAP -0.24 0.00169 NA
3 hsa-miR-361-5p SGK1 0.23 0.00962 -1.42 0 miRanda -0.49 2.0E-5 NA

Over-represented Gene Ontology Biological Process

NumGOOverlapSizeP ValueAdj. P Value
1 CELL CYCLE 42 1316 1.281e-17 5.962e-14
2 CELL CYCLE PROCESS 38 1081 2.863e-17 6.66e-14
3 MITOTIC CELL CYCLE 29 766 5.041e-14 7.818e-11
4 CELL CYCLE PHASE TRANSITION 18 255 1.797e-13 2.09e-10
5 NEGATIVE REGULATION OF CELL CYCLE 22 433 2.549e-13 2.372e-10
6 CELL CYCLE G2 M PHASE TRANSITION 14 138 7.215e-13 5.595e-10
7 REGULATION OF CYTOSKELETON ORGANIZATION 22 502 4.813e-12 3.199e-09
8 REGULATION OF CELL CYCLE 29 949 1.025e-11 5.961e-09
9 REGULATION OF MICROTUBULE BASED PROCESS 16 243 1.235e-11 6.385e-09
10 REGULATION OF ORGANELLE ORGANIZATION 32 1178 1.571e-11 7.312e-09
11 NEGATIVE REGULATION OF ORGANELLE ORGANIZATION 18 387 1.897e-10 8.023e-08
12 REGULATION OF PROTEIN MODIFICATION PROCESS 36 1710 8.423e-10 3.266e-07
13 REGULATION OF TRANSFERASE ACTIVITY 26 946 1.374e-09 4.919e-07
14 NEGATIVE REGULATION OF CELL CYCLE PROCESS 13 214 3.047e-09 1.013e-06
15 REGULATION OF MICROTUBULE POLYMERIZATION OR DEPOLYMERIZATION 12 178 3.917e-09 1.215e-06
16 NEGATIVE REGULATION OF CYTOSKELETON ORGANIZATION 13 221 4.499e-09 1.308e-06
17 REGULATION OF CELL CYCLE PROCESS 19 558 1.011e-08 2.533e-06
18 CELL CYCLE CHECKPOINT 12 194 1.035e-08 2.533e-06
19 NEGATIVE REGULATION OF CELLULAR COMPONENT ORGANIZATION 21 684 9.646e-09 2.533e-06
20 CELL DIVISION 17 460 1.963e-08 4.349e-06
21 MICROTUBULE CYTOSKELETON ORGANIZATION 15 348 1.891e-08 4.349e-06
22 REGULATION OF MITOTIC CELL CYCLE 17 468 2.525e-08 5.34e-06
23 MITOTIC NUCLEAR DIVISION 15 361 3.073e-08 6.216e-06
24 ANAPHASE PROMOTING COMPLEX DEPENDENT CATABOLIC PROCESS 8 77 5.905e-08 1.07e-05
25 ORGANELLE FISSION 17 496 5.86e-08 1.07e-05
26 REGULATION OF CELL CYCLE ARREST 9 108 5.982e-08 1.07e-05
27 POSTTRANSCRIPTIONAL REGULATION OF GENE EXPRESSION 16 448 8.447e-08 1.456e-05
28 NEGATIVE REGULATION OF MITOTIC CELL CYCLE 11 199 1.374e-07 2.283e-05
29 POSITIVE REGULATION OF CELL CYCLE PROCESS 12 247 1.485e-07 2.383e-05
30 NEGATIVE REGULATION OF PROTEIN MODIFICATION PROCESS 18 616 2.521e-07 3.91e-05
31 ERBB2 SIGNALING PATHWAY 6 39 2.618e-07 3.929e-05
32 REGULATION OF LIGASE ACTIVITY 9 130 2.963e-07 4.308e-05
33 SIGNAL TRANSDUCTION IN RESPONSE TO DNA DAMAGE 8 96 3.334e-07 4.701e-05
34 PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS 9 134 3.835e-07 5.249e-05
35 REGULATION OF PHOSPHORUS METABOLIC PROCESS 30 1618 4.795e-07 6.375e-05
36 MITOTIC CELL CYCLE CHECKPOINT 9 139 5.233e-07 6.706e-05
37 SPINDLE ASSEMBLY 7 70 5.332e-07 6.706e-05
38 MICROTUBULE BASED PROCESS 16 522 6.586e-07 8.064e-05
39 G1 DNA DAMAGE CHECKPOINT 7 73 7.124e-07 8.499e-05
40 DNA INTEGRITY CHECKPOINT 9 146 7.921e-07 9.214e-05
41 POSITIVE REGULATION OF LIGASE ACTIVITY 8 110 9.5e-07 0.0001078
42 NEGATIVE REGULATION OF GENE EXPRESSION 28 1493 1.001e-06 0.0001109
43 PHOSPHATE CONTAINING COMPOUND METABOLIC PROCESS 33 1977 1.218e-06 0.0001267
44 POSITIVE REGULATION OF TRANSFERASE ACTIVITY 17 616 1.225e-06 0.0001267
45 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 31 1784 1.198e-06 0.0001267
46 NEGATIVE REGULATION OF MOLECULAR FUNCTION 23 1079 1.297e-06 0.0001312
47 NEGATIVE REGULATION OF NITROGEN COMPOUND METABOLIC PROCESS 28 1517 1.371e-06 0.0001358
48 NEGATIVE REGULATION OF PROTEIN METABOLIC PROCESS 23 1087 1.471e-06 0.0001426
49 POSITIVE REGULATION OF TOR SIGNALING 5 29 1.512e-06 0.0001435
50 REGULATION OF KINASE ACTIVITY 19 776 1.645e-06 0.0001531
51 POSITIVE REGULATION OF CELL CYCLE ARREST 7 85 2.015e-06 0.0001838
52 REGULATION OF PROTEIN COMPLEX DISASSEMBLY 10 217 2.713e-06 0.0002427
53 NEGATIVE REGULATION OF PROTEIN COMPLEX DISASSEMBLY 9 170 2.81e-06 0.0002467
54 PROTEASOMAL PROTEIN CATABOLIC PROCESS 11 271 2.907e-06 0.0002505
55 MACROMOLECULAR COMPLEX ASSEMBLY 26 1398 3.059e-06 0.0002588
56 POSITIVE REGULATION OF CELL CYCLE 12 332 3.371e-06 0.0002801
57 REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 11 280 3.977e-06 0.0003246
58 NEGATIVE REGULATION OF CELL CYCLE G1 S PHASE TRANSITION 7 98 5.242e-06 0.0004205
59 NEGATIVE REGULATION OF TRANSFERASE ACTIVITY 12 351 5.947e-06 0.000465
60 MITOTIC DNA INTEGRITY CHECKPOINT 7 100 5.996e-06 0.000465
61 POSITIVE REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS 9 192 7.583e-06 0.0005697
62 PROTEIN PHOSPHORYLATION 20 944 7.592e-06 0.0005697
63 NEGATIVE REGULATION OF CELL CYCLE PHASE TRANSITION 8 146 7.935e-06 0.000586
64 INTRACELLULAR SIGNAL TRANSDUCTION 27 1572 8.382e-06 0.0006094
65 NEGATIVE REGULATION OF CELL DEATH 19 872 8.853e-06 0.0006313
66 POSITIVE REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 9 196 8.955e-06 0.0006313
67 PHOSPHORYLATION 23 1228 1.109e-05 0.0007705
68 PROTEIN CATABOLIC PROCESS 15 579 1.15e-05 0.0007872
69 INTERSPECIES INTERACTION BETWEEN ORGANISMS 16 662 1.368e-05 0.0009095
70 SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 16 662 1.368e-05 0.0009095
71 NEGATIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 17 740 1.395e-05 0.0009142
72 REGULATION OF CELL CYCLE PHASE TRANSITION 11 321 1.444e-05 0.0009331
73 REGULATION OF NUCLEAR DIVISION 8 163 1.773e-05 0.001119
74 ERBB SIGNALING PATHWAY 6 79 1.779e-05 0.001119
75 CYTOSKELETON ORGANIZATION 18 838 1.887e-05 0.00117
76 REGULATION OF CELL DIVISION 10 272 1.968e-05 0.001205
77 MACROMOLECULE CATABOLIC PROCESS 19 926 2.049e-05 0.001238
78 REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS 10 274 2.096e-05 0.00125
79 REGULATION OF PROTEIN SERINE THREONINE KINASE ACTIVITY 13 470 2.315e-05 0.001363
80 SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR 7 127 2.868e-05 0.001668
81 PROTEIN UBIQUITINATION 15 629 3.018e-05 0.001734
82 PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 18 873 3.237e-05 0.001837
83 POSITIVE REGULATION OF PROTEIN MODIFICATION PROCESS 21 1135 3.36e-05 0.001884
84 CELLULAR RESPONSE TO DNA DAMAGE STIMULUS 16 720 3.792e-05 0.002101
85 POSITIVE REGULATION OF CELLULAR COMPONENT ORGANIZATION 21 1152 4.171e-05 0.002283
86 REGULATION OF RNA STABILITY 7 139 5.114e-05 0.002735
87 NEGATIVE REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 7 139 5.114e-05 0.002735
88 RIBONUCLEOPROTEIN COMPLEX BIOGENESIS 12 440 5.533e-05 0.002925
89 RIBOSOME BIOGENESIS 10 308 5.642e-05 0.00295
90 NEGATIVE REGULATION OF CATALYTIC ACTIVITY 17 829 5.834e-05 0.003016
91 CELLULAR RESPONSE TO OXYGEN LEVELS 7 143 6.123e-05 0.003097
92 RESPONSE TO OXYGEN LEVELS 10 311 6.118e-05 0.003097
93 CHROMOSOME ORGANIZATION 19 1009 6.552e-05 0.003278
94 REGULATION OF CELL DEATH 24 1472 6.631e-05 0.003282
95 GLOBAL GENOME NUCLEOTIDE EXCISION REPAIR 4 32 6.716e-05 0.003289
96 TRANSLATIONAL INITIATION 7 146 6.983e-05 0.003385
97 REGULATION OF CELL CYCLE G1 S PHASE TRANSITION 7 147 7.29e-05 0.003497
98 PEPTIDYL SERINE MODIFICATION 7 148 7.609e-05 0.003613
99 REGULATION OF PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS 6 103 7.993e-05 0.003757
100 POSITIVE REGULATION OF PROTEIN METABOLIC PROCESS 24 1492 8.186e-05 0.003809
101 REGULATION OF CELLULAR RESPONSE TO STRESS 15 691 8.733e-05 0.004023
102 POSITIVE REGULATION OF PROTEIN CATABOLIC PROCESS 9 263 8.985e-05 0.004099
103 POSITIVE REGULATION OF PHOSPHATE METABOLIC PROCESS 19 1036 9.285e-05 0.004154
104 POSITIVE REGULATION OF PHOSPHORUS METABOLIC PROCESS 19 1036 9.285e-05 0.004154
105 CELL CYCLE ARREST 7 154 9.766e-05 0.004324
106 PROTEIN COMPLEX BIOGENESIS 20 1132 9.944e-05 0.004324
107 PROTEIN COMPLEX ASSEMBLY 20 1132 9.944e-05 0.004324
108 REGULATION OF TOR SIGNALING 5 68 0.0001069 0.004608
109 MITOTIC SPINDLE ORGANIZATION 5 69 0.0001147 0.004895
110 CHROMOSOME SEGREGATION 9 272 0.000116 0.004906
111 REGULATION OF CELLULAR PROTEIN LOCALIZATION 13 552 0.0001188 0.004981
112 REGULATION OF SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR 7 162 0.0001339 0.005564
113 ACTIVATION OF ANAPHASE PROMOTING COMPLEX ACTIVITY 3 15 0.0001376 0.005667
114 MEMBRANE ORGANIZATION 17 899 0.0001557 0.006354
115 ORGANELLE ASSEMBLY 12 495 0.0001677 0.006785
116 CELLULAR RESPONSE TO STRESS 24 1565 0.0001703 0.006829
117 MITOTIC SPINDLE ASSEMBLY 4 41 0.0001803 0.006989
118 MICROTUBULE CYTOSKELETON ORGANIZATION INVOLVED IN MITOSIS 4 41 0.0001803 0.006989
119 POSITIVE REGULATION OF CANONICAL WNT SIGNALING PATHWAY 6 119 0.0001773 0.006989
120 REGULATION OF CELLULAR AMIDE METABOLIC PROCESS 10 354 0.0001771 0.006989
121 CARBOHYDRATE BIOSYNTHETIC PROCESS 6 121 0.0001942 0.007405
122 PROTEIN DNA COMPLEX SUBUNIT ORGANIZATION 8 229 0.0001936 0.007405
123 SISTER CHROMATID SEGREGATION 7 176 0.0002233 0.008446
124 PEPTIDYL AMINO ACID MODIFICATION 16 841 0.0002298 0.008622
125 NEGATIVE REGULATION OF ERBB SIGNALING PATHWAY 4 44 0.0002378 0.00878
126 PROTEIN LOCALIZATION 26 1805 0.0002387 0.00878
127 DNA METABOLIC PROCESS 15 758 0.0002396 0.00878
NumGOOverlapSizeP ValueAdj. P Value
1 ENZYME BINDING 36 1737 1.288e-09 1.196e-06
2 KINASE BINDING 19 606 3.767e-08 1.75e-05
3 PROTEIN SERINE THREONINE KINASE ACTIVITY 15 445 4.591e-07 0.0001422
4 POLY A RNA BINDING 23 1170 5.042e-06 0.001171
5 KINASE ACTIVITY 18 842 2.01e-05 0.003734
6 PROTEIN KINASE ACTIVITY 15 640 3.681e-05 0.0057
7 IDENTICAL PROTEIN BINDING 21 1209 8.328e-05 0.007508
8 CYCLIN DEPENDENT PROTEIN KINASE ACTIVITY 4 34 8.569e-05 0.007508
9 RIBONUCLEOTIDE BINDING 28 1860 6.129e-05 0.007508
10 MACROMOLECULAR COMPLEX BINDING 23 1399 8.488e-05 0.007508
11 RNA BINDING 25 1598 8.889e-05 0.007508
NumGOOverlapSizeP ValueAdj. P Value
1 MICROTUBULE CYTOSKELETON 26 1068 1.686e-08 9.847e-06
2 CONDENSED NUCLEAR CHROMOSOME 8 85 1.289e-07 3.765e-05
3 CHROMOSOME 21 880 6.653e-07 0.0001162
4 SPINDLE 12 289 7.96e-07 0.0001162
5 CYTOSKELETON 33 1967 1.088e-06 0.0001271
6 CYTOSKELETAL PART 27 1436 1.547e-06 0.000129
7 MICROTUBULE ORGANIZING CENTER 17 623 1.429e-06 0.000129
8 SPINDLE MICROTUBULE 6 58 2.916e-06 0.0002129
9 NUCLEAR CHROMOSOME 15 523 3.403e-06 0.0002208
10 CENTROSOME 14 487 7.159e-06 0.0004181
11 CONDENSED CHROMOSOME 9 195 8.594e-06 0.0004562
12 RIBONUCLEOPROTEIN COMPLEX 17 721 9.967e-06 0.000485
13 MICROTUBULE 12 405 2.478e-05 0.001113
14 CHROMATIN 12 441 5.654e-05 0.002359
15 TOR COMPLEX 3 13 8.739e-05 0.003402
16 CHROMOSOMAL REGION 10 330 9.996e-05 0.003649
17 SPINDLE POLE 6 126 0.0002419 0.007888
18 CONDENSED NUCLEAR CHROMOSOME CENTROMERIC REGION 3 18 0.0002431 0.007888

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 hsa04110_Cell_cycle 10 128 2e-08 3.601e-06
2 hsa04114_Oocyte_meiosis 8 114 1.247e-06 0.0001122
3 hsa04914_Progesterone.mediated_oocyte_maturation 5 87 0.0003414 0.02049
4 hsa04115_p53_signaling_pathway 4 69 0.001326 0.05965
5 hsa04120_Ubiquitin_mediated_proteolysis 5 139 0.002794 0.0819
6 hsa04151_PI3K_AKT_signaling_pathway 8 351 0.00306 0.0819
7 hsa04540_Gap_junction 4 90 0.003506 0.0819
8 hsa03010_Ribosome 4 92 0.003793 0.0819
9 hsa03013_RNA_transport 5 152 0.004095 0.0819
10 hsa00030_Pentose_phosphate_pathway 2 27 0.01482 0.2668
11 hsa04390_Hippo_signaling_pathway 4 154 0.0221 0.3616
12 hsa04916_Melanogenesis 3 101 0.03282 0.4662
13 hsa04960_Aldosterone.regulated_sodium_reabsorption 2 42 0.034 0.4662
14 hsa00310_Lysine_degradation 2 44 0.03702 0.4662
15 hsa04660_T_cell_receptor_signaling_pathway 3 108 0.03885 0.4662
16 hsa04722_Neurotrophin_signaling_pathway 3 127 0.05781 0.6244
17 hsa00140_Steroid_hormone_biosynthesis 2 57 0.05897 0.6244
18 hsa04910_Insulin_signaling_pathway 3 138 0.07045 0.7045
19 hsa03320_PPAR_signaling_pathway 2 70 0.08428 0.7815
20 hsa04310_Wnt_signaling_pathway 3 151 0.08683 0.7815
21 hsa04662_B_cell_receptor_signaling_pathway 2 75 0.09475 0.7928
22 hsa04370_VEGF_signaling_pathway 2 76 0.09689 0.7928
23 hsa04664_Fc_epsilon_RI_signaling_pathway 2 79 0.1034 0.8091
24 hsa03015_mRNA_surveillance_pathway 2 83 0.1122 0.8394
25 hsa04012_ErbB_signaling_pathway 2 87 0.1212 0.8394
26 hsa04912_GnRH_signaling_pathway 2 101 0.1541 0.9625
27 hsa04510_Focal_adhesion 3 200 0.1604 0.9625
28 hsa03040_Spliceosome 2 128 0.2211 1
29 hsa04360_Axon_guidance 2 130 0.2262 1
30 hsa04530_Tight_junction 2 133 0.2338 1
31 hsa04650_Natural_killer_cell_mediated_cytotoxicity 2 136 0.2414 1
32 hsa04010_MAPK_signaling_pathway 3 268 0.2822 1
33 hsa04141_Protein_processing_in_endoplasmic_reticulum 2 168 0.323 1
34 hsa04062_Chemokine_signaling_pathway 2 189 0.3755 1
35 hsa04144_Endocytosis 2 203 0.4096 1
36 hsa04014_Ras_signaling_pathway 2 236 0.4861 1

Quest ID: 9acaf845fac1dc113fcc18d787dce2ff