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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-26b-5p TMCO3 -1.11 0 1.06 0 miRNAWalker2 validate -0.26 6.0E-5 NA
2 hsa-miR-3607-3p TMCO3 -2.16 0 1.06 0 MirTarget -0.16 0 NA
NumGOOverlapSizeP ValueAdj. P Value
1 NEGATIVE REGULATION OF TYPE I INTERFERON PRODUCTION 4 40 1.181e-07 0.0003043
2 TRANSLESION SYNTHESIS 4 41 1.308e-07 0.0003043
3 POSTREPLICATION REPAIR 4 54 4.045e-07 0.0006274
4 CELLULAR CATABOLIC PROCESS 10 1322 7.95e-07 0.0009248
5 ERROR FREE TRANSLESION SYNTHESIS 3 19 1.272e-06 0.0009635
6 DNA SYNTHESIS INVOLVED IN DNA REPAIR 4 74 1.45e-06 0.0009635
7 ERROR PRONE TRANSLESION SYNTHESIS 3 19 1.272e-06 0.0009635
8 NUCLEOTIDE EXCISION REPAIR DNA DAMAGE RECOGNITION 3 23 2.318e-06 0.001165
9 GLYCOGEN BIOSYNTHETIC PROCESS 3 25 3.005e-06 0.001165
10 NUCLEOTIDE EXCISION REPAIR DNA GAP FILLING 3 24 2.647e-06 0.001165
11 GLUCAN BIOSYNTHETIC PROCESS 3 25 3.005e-06 0.001165
12 NUCLEOTIDE EXCISION REPAIR DNA DUPLEX UNWINDING 3 22 2.017e-06 0.001165
13 REGULATION OF NECROTIC CELL DEATH 3 26 3.395e-06 0.001215
14 TRANSFORMING GROWTH FACTOR BETA RECEPTOR SIGNALING PATHWAY 4 95 3.947e-06 0.001312
15 NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR SIGNALING PATHWAY 3 28 4.271e-06 0.001325
16 NUCLEOTIDE EXCISION REPAIR PREINCISION COMPLEX ASSEMBLY 3 29 4.76e-06 0.001384
17 MACROMOLECULE CATABOLIC PROCESS 8 926 5.396e-06 0.001395
18 MYD88 INDEPENDENT TOLL LIKE RECEPTOR SIGNALING PATHWAY 3 30 5.285e-06 0.001395
19 MYD88 DEPENDENT TOLL LIKE RECEPTOR SIGNALING PATHWAY 3 32 6.447e-06 0.001429
20 GLOBAL GENOME NUCLEOTIDE EXCISION REPAIR 3 32 6.447e-06 0.001429
21 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER IN RESPONSE TO HYPOXIA 3 32 6.447e-06 0.001429
22 CYTOPLASMIC PATTERN RECOGNITION RECEPTOR SIGNALING PATHWAY 3 33 7.087e-06 0.001484
23 REGULATION OF TYPE I INTERFERON PRODUCTION 4 111 7.335e-06 0.001484
24 NUCLEOTIDE EXCISION REPAIR 4 113 7.874e-06 0.001527
25 DNA DAMAGE RESPONSE DETECTION OF DNA DAMAGE 3 36 9.253e-06 0.001656
26 POSITIVE REGULATION OF ERBB SIGNALING PATHWAY 3 36 9.253e-06 0.001656
27 DNA BIOSYNTHETIC PROCESS 4 121 1.033e-05 0.001716
28 VIRION ASSEMBLY 3 37 1.006e-05 0.001716
29 ERBB2 SIGNALING PATHWAY 3 39 1.182e-05 0.001774
30 NUCLEOTIDE EXCISION REPAIR DNA INCISION 3 39 1.182e-05 0.001774
31 CATABOLIC PROCESS 10 1773 1.136e-05 0.001774
32 POLYSACCHARIDE BIOSYNTHETIC PROCESS 3 42 1.481e-05 0.002154
33 NEGATIVE REGULATION OF ERBB SIGNALING PATHWAY 3 44 1.706e-05 0.002335
34 INTERSTRAND CROSS LINK REPAIR 3 44 1.706e-05 0.002335
35 NEGATIVE REGULATION OF PROTEIN MODIFICATION BY SMALL PROTEIN CONJUGATION OR REMOVAL 4 139 1.785e-05 0.002374
36 RESPONSE TO TRANSFORMING GROWTH FACTOR BETA 4 144 2.052e-05 0.002652
37 REGULATION OF TUMOR NECROSIS FACTOR MEDIATED SIGNALING PATHWAY 3 50 2.514e-05 0.003161
38 CELLULAR CARBOHYDRATE BIOSYNTHETIC PROCESS 3 51 2.669e-05 0.003268
39 CELLULAR GLUCAN METABOLIC PROCESS 3 58 3.933e-05 0.004464
40 PROTEIN CATABOLIC PROCESS 6 579 3.803e-05 0.004464
41 GLUCAN METABOLIC PROCESS 3 58 3.933e-05 0.004464
42 OXIDATION REDUCTION PROCESS 7 898 4.681e-05 0.005186
43 INNATE IMMUNE RESPONSE 6 619 5.522e-05 0.005975
44 NEGATIVE REGULATION OF CELLULAR RESPONSE TO TRANSFORMING GROWTH FACTOR BETA STIMULUS 3 66 5.798e-05 0.005996
45 NEGATIVE REGULATION OF TRANSFORMING GROWTH FACTOR BETA RECEPTOR SIGNALING PATHWAY 3 66 5.798e-05 0.005996
46 REGULATION OF DNA TEMPLATED TRANSCRIPTION IN RESPONSE TO STRESS 3 67 6.066e-05 0.006006
47 TRANSMEMBRANE RECEPTOR PROTEIN SERINE THREONINE KINASE SIGNALING PATHWAY 4 190 6.066e-05 0.006006
48 MULTI ORGANISM TRANSPORT 3 68 6.341e-05 0.006021
49 MULTI ORGANISM LOCALIZATION 3 68 6.341e-05 0.006021
50 I KAPPAB KINASE NF KAPPAB SIGNALING 3 70 6.915e-05 0.006436
51 ENERGY RESERVE METABOLIC PROCESS 3 72 7.523e-05 0.006781
52 TRANSCRIPTION COUPLED NUCLEOTIDE EXCISION REPAIR 3 73 7.84e-05 0.006781
53 G1 DNA DAMAGE CHECKPOINT 3 73 7.84e-05 0.006781
54 INTERSPECIES INTERACTION BETWEEN ORGANISMS 6 662 8.015e-05 0.006781
55 SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 6 662 8.015e-05 0.006781
56 REGULATION OF VIRAL GENOME REPLICATION 3 75 8.499e-05 0.007062
57 ANAPHASE PROMOTING COMPLEX DEPENDENT CATABOLIC PROCESS 3 77 9.193e-05 0.007375
58 NEGATIVE REGULATION OF CYTOKINE PRODUCTION 4 211 9.109e-05 0.007375
59 ERBB SIGNALING PATHWAY 3 79 9.923e-05 0.007826
60 POLYSACCHARIDE METABOLIC PROCESS 3 80 0.000103 0.007858
61 ENERGY DERIVATION BY OXIDATION OF ORGANIC COMPOUNDS 4 217 0.0001015 0.007858
62 DNA GEOMETRIC CHANGE 3 81 0.0001069 0.008023
63 JNK CASCADE 3 82 0.0001109 0.008189
64 REGULATION OF ERBB SIGNALING PATHWAY 3 83 0.000115 0.008229
65 NIK NF KAPPAB SIGNALING 3 83 0.000115 0.008229
66 FIBROBLAST GROWTH FACTOR RECEPTOR SIGNALING PATHWAY 3 84 0.0001191 0.008398
67 TOLL LIKE RECEPTOR SIGNALING PATHWAY 3 85 0.0001234 0.008443
68 POSITIVE REGULATION OF CELL CYCLE ARREST 3 85 0.0001234 0.008443
69 CYTOKINE MEDIATED SIGNALING PATHWAY 5 452 0.0001386 0.009346
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value

Quest ID: 01de37030a63d6931a4ae3790f14d6b0