Cancer Genetics and Epigenetics 2016, Vol.4, No.1, 1-10
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Function of ncRNA
Multiple-network includes 18,751 co-expression relationships between ncRNAs and protein-coding genes. There
are 369 ncRNAs co-expressed with more than 10 coding-genes. We predicted these 369 ncRNAs function from
the function annotation information of neighbor nodes by bioinformatics tool Database for Annotation,
Visualization, and Integrated Discovery (DAVID) (Huang et al., 2009). There are 339 ncRNAs enriched to at least
one GO term (Table 2, Supplement 1), each ncRNA average enriched to 30 GO terms. We find these ncRNA
functions mainly include metabolism, development, expression and regulation, transport, and there are 94
ncRNAs enriched to GO terms which are associated with ion channel, such as ion transport, channel activity, ion
transmembrane transport and so on.
Table 2 Function annotation of ncRNA (Partial results)
ncRNA
Term name
P value
CTB-43P18.1
generation of precursor metabolites and energy
7.40E-24
RP11-770J1.5
oxidative phosphorylation
1.31E-17
RP11-473O4.5
generation of precursor metabolites and energy
1.58E-17
RP5-940J5.9
generation of precursor metabolites and energy
4.04E-13
AC009501.4
generation of precursor metabolites and energy
6.17E-09
RP1-101D8.1
oxidative phosphorylation
4.15E-08
RP11-161H23.5
mitochondrial membrane
4.50E-08
AC002398.11
transcription factor activity
8.29E-08
RP13-514E23.1
generation of precursor metabolites and energy
2.38E-07
RP5-1172N10.4
oxidative phosphorylation
5.70E-07
RP11-386G11.10
mitochondrial membrane
5.95E-07
RP11-115D19.1
generation of precursor metabolites and energy
8.46E-07
LINC01566
oxidative phosphorylation
1.89E-06
LINC00202-2
ion transport
2.06E-06
RP11-620J15.4
receptor complex
2.09E-06
LINC01271
plasma membrane part
3.26E-06
Relations between ncRNAs and ion channels
We extract genes co-expressed with potassium channel protein gene, sodium channel protein gene, calcium
channel protein gene, chloride channel protein gene from multiple-network (Figure 4). According to the previous
results, based on neighbor node predict ncRNA functions, we found that most of functions of ncRNAs
co-expressed with ion channel protein gene are associated with function of cell membrane, ion transport. In the
multiple-network, there are 19 potassium channel protein genes, and 540 genes co-expressed with them (Figure
4A). In total of 60 ncRNAs that co-expression with potassium channel protein genes, of which 54 ncRNAs
enrichment to at least 1 GO term. These GO terms are associated with functions of cell membrane, plasma
membrane, ion transport, cation transporter. For example, lncRNA LINC00202-2 enrichment to 72 GO terms
which mainly include ion transport, membrane composition, cation transporter, metal ion transport, gated channel
activity. There are 410 coding-genes and 96 ncRNAs co-expression with 15 calcium channel genes in
multiple-network (Figure 4B). 85 ncRNAs enrichment at least one GO term which are related on fuction of
membrane component, ion transport. For example, ncRNA RP4-761J14.8 enrichment to 10 GO terms, these GO
term mainly include ion transport, metal ion transport, 2-, 3- monovalent inorganic cation transporter, cation
transporter, transition metal cation transporter(Figure 5B). We analyzed sodium channel gene in multiple-network,
found 3 sodium channel genes are co-expressed with 160 coding-genes and 49 ncRNAs (Figure 4C). 47 ncRNAs
enrichment to at least one GO term. These GO term mainly include transcriptional regulation, DNA binding,
membrane component, ion transport and so on (Figure 5C). Moreover, there are 4 chloride channel genes
