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-127-3p CENPA -1.21 0 2.97 0 miRanda -0.16 0.02407 NA
2 hsa-miR-199a-5p CENPA -1.65 0 2.97 0 miRanda -0.36 0 NA
NumGOOverlapSizeP ValueAdj. P Value
1 CHROMATIN ORGANIZATION 22 663 9.338e-19 4.345e-15
2 CHROMOSOME ORGANIZATION 23 1009 4.567e-16 1.063e-12
3 CHROMATIN MODIFICATION 18 539 2.43e-15 3.769e-12
4 COVALENT CHROMATIN MODIFICATION 12 345 1.294e-10 1.505e-07
5 REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 21 1784 3.47e-09 3.229e-06
6 CHROMATIN REMODELING 7 150 1.741e-07 0.000135
7 NEGATIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 12 740 6.121e-07 0.0004069
8 NEGATIVE REGULATION OF NITROGEN COMPOUND METABOLIC PROCESS 16 1517 1.928e-06 0.001068
9 PEPTIDYL LYSINE MODIFICATION 8 312 2.065e-06 0.001068
10 NEGATIVE REGULATION OF GENE EXPRESSION 15 1493 7.969e-06 0.003708
11 POSITIVE REGULATION OF GENE EXPRESSION 16 1733 1.072e-05 0.004537
12 POSITIVE REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER 12 1004 1.421e-05 0.005511
13 POSITIVE REGULATION OF BIOSYNTHETIC PROCESS 16 1805 1.79e-05 0.006405
NumGOOverlapSizeP ValueAdj. P Value
1 CHROMATIN BINDING 11 435 2.298e-08 1.068e-05
2 MACROMOLECULAR COMPLEX BINDING 18 1399 1.72e-08 1.068e-05
3 REGULATORY REGION NUCLEIC ACID BINDING 11 818 1.153e-05 0.003572
NumGOOverlapSizeP ValueAdj. P Value
1 NUCLEAR CHROMATIN 9 291 9.139e-08 2.669e-05
2 CATALYTIC COMPLEX 15 1038 8.122e-08 2.669e-05
3 CHROMATIN 10 441 2.956e-07 5.589e-05
4 NUCLEOPLASM PART 12 708 3.828e-07 5.589e-05
5 NUCLEAR CHROMOSOME 10 523 1.395e-06 0.0001629
6 TRANSFERASE COMPLEX 11 703 2.733e-06 0.000266
7 CHROMOSOME 12 880 3.732e-06 0.0003114
8 NUCLEAR HETEROCHROMATIN 3 32 9.224e-05 0.006734

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 hsa04120_Ubiquitin_mediated_proteolysis 4 139 0.0005789 0.09613
2 hsa04520_Adherens_junction 3 73 0.001068 0.09613
3 hsa04310_Wnt_signaling_pathway 3 151 0.008308 0.4985
4 hsa04510_Focal_adhesion 3 200 0.01766 0.7946
5 hsa04916_Melanogenesis 2 101 0.03153 1
6 hsa04110_Cell_cycle 2 128 0.04843 1
7 hsa04390_Hippo_signaling_pathway 2 154 0.06712 1
8 hsa04630_Jak.STAT_signaling_pathway 2 155 0.06788 1

Quest ID: 76ace6da116a14725fa1336ec2cb4988