Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis

BMC Bioinformatics

Table 1 Properties of the chromatin graph

chr	no.cc	Min cc csize	Mean cc csize	Max cc csize	Number of nodes containing lncRNA	Nodes containing lncRNA involved in interactions	Node containing lncRNA with highest degree	Degree
chr1	1765	1	3.35	503	444	404	RP11-442N24__B.1,RNU11	26
chr2	1264	1	2.77	64	299	250	ZFP36L2	19
chr3	994	1	2.82	70	213	185	TERC	13
chr4	649	1	2.66	52	160	127	RP11-539L10.3,AC093323.3	9
chr5	890	1	2.71	43	245	197	ARRDC3	15
chr6	1172	1	3.21	337	208	190	ABT1	14
chr7	1016	1	2.76	88	196	164	LINC01287	14
chr8	619	1	2.87	105	187	159	YWHAZ	20
chr9	505	1	3.1	141	127	118	SNHG7	11
chr10	685	1	2.84	92	144	126	VIM	9
chr11	858	1	3.03	128	216	188	BEST1,FTH1	12
chr12	655	1	3.25	69	224	199	BTG1	22
chr13	280	1	2.45	39	62	51	MIR17HG	21
chr14	357	1	2.98	36	131	115	PRMT5	10
chr15	430	1	3	72	156	132	GABPB1	9
chr16	457	1	3.63	196	182	166	RAB26,TRAF7	17
chr17	517	1	4.3	350	275	267	LINC00910	17
chr18	278	1	2.61	71	61	47	MYL12A	17
chr19	380	1	5.36	158	227	220	SLC1A5	15
chr20	407	1	3.18	90	109	99	CEBPB	26
chr21	207	1	3.02	53	73	62	DYRK1A	7
chr22	279	1	3.24	67	84	78	POLDIP3	20
chrX	358	1	2.75	60	57	49	VSIG4	10

For each chromosome we report: the total number of connected components (no.cc), the minimum number of nodes (min cc csize), the average number of nodes (mean cc csize) and maximum number of nodes (max cc csize)) of the connected components, the total number of annotated lncRNAs (number of lncRNAs), the total number of lncRNAs which are involved in at least one interaction (lncRNAs in interactions), the lncRNA gene symbol of the highest degree’s lncRNAs (lncRNA with highest degree) and the actual highest degree value for that lncRNA (degree)

ISSN: 1471-2105