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show label of nodes with degree >=

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gravity >=

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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-129-5p SPARCL1 -0.52 0.22258 -3.4 0 miRanda -0.12 0.00496 NA
2 hsa-miR-140-5p SPARCL1 0.84 4.0E-5 -3.4 0 miRanda -0.26 0.00279 NA
3 hsa-miR-98-5p SPARCL1 1.11 0 -3.4 0 miRNAWalker2 validate -0.71 0 NA
NumGOOverlapSizeP ValueAdj. P Value
1 ATP GENERATION FROM ADP 3 39 8.149e-07 0.0007583
2 NADH METABOLIC PROCESS 3 35 5.842e-07 0.0007583
3 GLUCOSE METABOLIC PROCESS 4 119 2.434e-07 0.0007583
4 HEXOSE METABOLIC PROCESS 4 157 7.398e-07 0.0007583
5 GLUCOSE CATABOLIC PROCESS 3 29 3.267e-07 0.0007583
6 SMALL MOLECULE BIOSYNTHETIC PROCESS 5 443 1.199e-06 0.0009295
7 ADP METABOLIC PROCESS 3 47 1.443e-06 0.000953
8 HEXOSE CATABOLIC PROCESS 3 49 1.638e-06 0.000953
9 NAD METABOLIC PROCESS 3 55 2.329e-06 0.0009854
10 MONOSACCHARIDE BIOSYNTHETIC PROCESS 3 54 2.203e-06 0.0009854
11 MONOSACCHARIDE METABOLIC PROCESS 4 202 2.023e-06 0.0009854
12 MONOSACCHARIDE CATABOLIC PROCESS 3 59 2.884e-06 0.001118
13 NUCLEOTIDE PHOSPHORYLATION 3 61 3.191e-06 0.001142
14 PYRUVATE METABOLIC PROCESS 3 65 3.868e-06 0.0012
15 RIBONUCLEOSIDE DIPHOSPHATE METABOLIC PROCESS 3 64 3.691e-06 0.0012
16 ORGANONITROGEN COMPOUND METABOLIC PROCESS 7 1796 4.379e-06 0.001274
17 NUCLEOSIDE DIPHOSPHATE METABOLIC PROCESS 3 84 8.396e-06 0.002298
18 OXIDOREDUCTION COENZYME METABOLIC PROCESS 3 107 1.738e-05 0.004494
19 CARBOHYDRATE CATABOLIC PROCESS 3 113 2.047e-05 0.005014
20 GLYCOSYL COMPOUND METABOLIC PROCESS 4 368 2.169e-05 0.005047
21 FRUCTOSE METABOLIC PROCESS 2 15 2.354e-05 0.005217
22 CARBOHYDRATE BIOSYNTHETIC PROCESS 3 121 2.513e-05 0.005315
23 PURINE CONTAINING COMPOUND METABOLIC PROCESS 4 394 2.836e-05 0.005737
24 ORGANOPHOSPHATE METABOLIC PROCESS 5 885 3.51e-05 0.006805
25 SINGLE ORGANISM CATABOLIC PROCESS 5 957 5.114e-05 0.009519
NumGOOverlapSizeP ValueAdj. P Value
NumGOOverlapSizeP ValueAdj. P Value

Over-represented Pathway

NumPathwayPathviewOverlapSizeP ValueAdj. P Value
1 hsa00010_Glycolysis_._Gluconeogenesis 3 65 3.868e-06 0.0006963
2 hsa00030_Pentose_phosphate_pathway 2 27 7.845e-05 0.007061
3 hsa00051_Fructose_and_mannose_metabolism 2 36 0.0001405 0.008429
4 hsa03013_RNA_transport 2 152 0.002481 0.1116

Quest ID: 61122efe670210bdff24e4a17f7c1e96