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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-5p BRCC3 0.6 0.01023 0.16 0.30814 miRanda -0.13 5.0E-5 NA
2 hsa-miR-218-5p BRCC3 -0.57 0.0552 0.16 0.30814 MirTarget; miRNATAP -0.12 0 NA
3 hsa-miR-23b-3p BRCC3 -0.25 0.1502 0.16 0.30814 MirTarget -0.14 0.00084 NA
NumGOOverlapSizeP ValueAdj. P Value
1 TRANSLATIONAL INITIATION 13 146 6.693e-19 3.114e-15
2 MULTI ORGANISM METABOLIC PROCESS 12 138 2.386e-17 5.552e-14
3 ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM 10 104 5.205e-15 6.458e-12
4 VIRAL LIFE CYCLE 13 290 5.552e-15 6.458e-12
5 PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM 10 123 2.917e-14 2.715e-11
6 PROTEIN TARGETING TO MEMBRANE 10 157 3.479e-13 2.698e-10
7 RIBONUCLEOPROTEIN COMPLEX BIOGENESIS 13 440 1.146e-12 6.751e-10
8 NUCLEAR TRANSCRIBED MRNA CATABOLIC PROCESS NONSENSE MEDIATED DECAY 9 118 1.161e-12 6.751e-10
9 PEPTIDE METABOLIC PROCESS 14 571 1.597e-12 8.257e-10
10 AMIDE BIOSYNTHETIC PROCESS 13 507 6.82e-12 3.174e-09
11 INTERSPECIES INTERACTION BETWEEN ORGANISMS 14 662 1.161e-11 4.501e-09
12 SYMBIOSIS ENCOMPASSING MUTUALISM THROUGH PARASITISM 14 662 1.161e-11 4.501e-09
13 CELLULAR AMIDE METABOLIC PROCESS 14 727 4.034e-11 1.444e-08
14 ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE 10 264 6.15e-11 2.044e-08
15 RNA CATABOLIC PROCESS 9 227 4.205e-10 1.304e-07
16 RRNA METABOLIC PROCESS 9 255 1.174e-09 3.413e-07
17 ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE 10 361 1.294e-09 3.542e-07
18 PROTEIN LOCALIZATION TO MEMBRANE 10 376 1.916e-09 4.952e-07
19 NCRNA PROCESSING 10 386 2.465e-09 6.037e-07
20 PROTEIN TARGETING 10 406 4.001e-09 9.309e-07
21 RIBOSOME BIOGENESIS 9 308 6.124e-09 1.357e-06
22 CELLULAR MACROMOLECULAR COMPLEX ASSEMBLY 12 727 7.713e-09 1.631e-06
23 MACROMOLECULE CATABOLIC PROCESS 13 926 1.094e-08 2.213e-06
24 ORGANONITROGEN COMPOUND BIOSYNTHETIC PROCESS 13 1024 3.606e-08 6.99e-06
25 NCRNA METABOLIC PROCESS 10 533 5.271e-08 9.81e-06
26 PROTEIN LOCALIZATION TO ORGANELLE 10 556 7.825e-08 1.4e-05
27 CELLULAR CATABOLIC PROCESS 14 1322 8.938e-08 1.485e-05
28 FORMATION OF TRANSLATION PREINITIATION COMPLEX 4 22 8.803e-08 1.485e-05
29 ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS 9 427 1.018e-07 1.633e-05
30 MACROMOLECULAR COMPLEX ASSEMBLY 14 1398 1.786e-07 2.77e-05
31 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER IN RESPONSE TO HYPOXIA 4 32 4.267e-07 6.405e-05
32 ORGANONITROGEN COMPOUND METABOLIC PROCESS 15 1796 5.898e-07 8.576e-05
33 MEMBRANE ORGANIZATION 11 899 7.501e-07 0.0001027
34 SINGLE ORGANISM CELLULAR LOCALIZATION 11 898 7.419e-07 0.0001027
35 ESTABLISHMENT OF PROTEIN LOCALIZATION 13 1423 1.6e-06 0.0002127
36 INTRACELLULAR PROTEIN TRANSPORT 10 781 1.768e-06 0.0002286
37 MRNA METABOLIC PROCESS 9 611 2.04e-06 0.0002566
38 RIBONUCLEOPROTEIN COMPLEX SUBUNIT ORGANIZATION 6 199 2.233e-06 0.0002735
39 RNA PROCESSING 10 835 3.219e-06 0.0003745
40 CATABOLIC PROCESS 14 1773 3.159e-06 0.0003745
41 PROTEIN UBIQUITINATION INVOLVED IN UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS 5 134 6.006e-06 0.0006816
42 PROTEIN POLYUBIQUITINATION 6 243 7.053e-06 0.0007814
43 REGULATION OF DNA TEMPLATED TRANSCRIPTION IN RESPONSE TO STRESS 4 67 8.661e-06 0.0009372
44 NUCLEOTIDE EXCISION REPAIR DNA DUPLEX UNWINDING 3 22 1.029e-05 0.001088
45 NUCLEOTIDE EXCISION REPAIR DNA DAMAGE RECOGNITION 3 23 1.182e-05 0.001222
46 REGULATION OF TRANSLATIONAL INITIATION 4 82 1.935e-05 0.001958
47 PROTEIN LOCALIZATION 13 1805 2.177e-05 0.002155
48 POSTTRANSCRIPTIONAL REGULATION OF GENE EXPRESSION 7 448 2.234e-05 0.002165
49 NUCLEOTIDE EXCISION REPAIR PREINCISION COMPLEX ASSEMBLY 3 29 2.419e-05 0.002297
50 GLOBAL GENOME NUCLEOTIDE EXCISION REPAIR 3 32 3.27e-05 0.003043
51 DNA DAMAGE RESPONSE DETECTION OF DNA DAMAGE 3 36 4.681e-05 0.004189
52 POSITIVE REGULATION OF ERBB SIGNALING PATHWAY 3 36 4.681e-05 0.004189
53 VIRION ASSEMBLY 3 37 5.088e-05 0.004467
54 NUCLEOTIDE EXCISION REPAIR DNA INCISION 3 39 5.968e-05 0.005142
55 POSITIVE REGULATION OF LIGASE ACTIVITY 4 110 6.142e-05 0.005196
56 NUCLEOTIDE EXCISION REPAIR 4 113 6.822e-05 0.005668
57 PROTEOLYSIS 10 1208 7.9e-05 0.006449
58 CELLULAR MACROMOLECULE LOCALIZATION 10 1234 9.439e-05 0.007573
59 REGULATION OF LIGASE ACTIVITY 4 130 0.0001175 0.009268
NumGOOverlapSizeP ValueAdj. P Value
1 STRUCTURAL CONSTITUENT OF RIBOSOME 9 212 2.293e-10 2.13e-07
2 RNA BINDING 14 1598 9.13e-07 0.0004241
3 TRANSLATION INITIATION FACTOR ACTIVITY 4 51 2.888e-06 0.0008942
4 POLY A RNA BINDING 11 1170 9.617e-06 0.001787
5 STRUCTURAL MOLECULE ACTIVITY 9 732 8.865e-06 0.001787
6 TRANSLATION FACTOR ACTIVITY RNA BINDING 4 89 2.675e-05 0.004142
NumGOOverlapSizeP ValueAdj. P Value
1 CYTOSOLIC RIBOSOME 9 113 7.803e-13 4.557e-10
2 RIBOSOMAL SUBUNIT 9 163 2.183e-11 6.375e-09
3 RIBOSOME 9 226 4.044e-10 5.904e-08
4 CYTOSOLIC PART 9 223 3.592e-10 5.904e-08
5 RIBONUCLEOPROTEIN COMPLEX 13 721 5.332e-10 6.228e-08
6 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 COMPLEX 4 16 2.209e-08 1.843e-06
7 TRANSLATION PREINITIATION COMPLEX 4 16 2.209e-08 1.843e-06
8 CYTOSOLIC LARGE RIBOSOMAL SUBUNIT 5 61 1.187e-07 8.665e-06
9 LARGE RIBOSOMAL SUBUNIT 5 95 1.102e-06 7.148e-05
10 CYTOSOLIC SMALL RIBOSOMAL SUBUNIT 4 44 1.584e-06 9.251e-05
11 SMALL RIBOSOMAL SUBUNIT 4 68 9.189e-06 0.0004878
12 NUCLEAR UBIQUITIN LIGASE COMPLEX 3 42 7.466e-05 0.003634

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 Oocyte_meiosis_hsa04114 3 124 0.001806 0.09393
2 Cell_cycle_hsa04110 2 124 0.02433 0.6326

Quest ID: 50edf97f02ac767d0732a291a8c35962