Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D

Supplementary Data

Konstantin Riege, Martin Hölzer, Tilman E. Klassert, Emanuel Barth, Julia Bräuer, Maximilian Collatz, Franziska Hufsky, Nelly Mostajo B., Magdalena Stock, Bertram Vogel, Hortense Slevogt, and Manja Marz

Contents

• S1: Samples preprocessing
• S2: Differential gene expression, pairwise DESeq2 comparisons
• S3: Known ncRNAs related to fungal infections from literature
• S4: Scatter plots of additional comparisons
• S5: Box plots of potential ncRNA marker genes
• S6: Antisense and lincRNA expression heat maps
• S7: Pathway heat map of antisense read counts
• S8: Differential expressed ncRNA isoforms
• S9: Comparison of different filter steps to detect significant differential expressed genes
• S10: Response element (RARE, VDRE) enrichment

S1: FastQC and SortMeRNA: quality control and search for rRNA in samples

Shown in Tab. S1 are the amount of raw and trimmed reads as well as the percentage of different rRNA classes found by SortMeRNA.

Overall 48 samples were collected from human monocytes after 6h uninfected (ctr), or post infection with C. albicans (can), A. fumigatus (asp) or E. coli (eco).

Additionally, some of the samples were either treated with all-trans-retinoic acid (atRA) or vitamin D (vitD).

We collected samples from four different patients (n2, n3, n5 and n6), used as biological replicates.

Nr	Sample	Description	# Reads (raw)	FastQC (raw)	# Reads (trimmed)	FastQC (trimmed)	rRNA 5s (%)	rRNA 5.8s (%)	rRNA 18s (%)	rRNA 28s (%)	∑ rRNA (%)
1	mono6_n2_ctr	Control, patient1	17928706	fastqc	17898783	fastqc	0.26	0.0	8.4	2.14	10.8
2	mono6_n3_ctr	Control, patient2	20033995	fastqc	20004690	fastqc	0.25	0.01	13.8	4.88	18.94
3	mono6_n5_ctr	Control, patient3	15939690	fastqc	15917133	fastqc	0.27	0.01	14.07	5.57	19.92
4	mono6_n6_ctr	Control, patient4	23376665	fastqc	23344468	fastqc	0.28	0.01	14.15	5.62	20.06
5	mono6_n2_atra	Control, atRA, patient1	20037397	fastqc	20003109	fastqc	0.21	0.0	7.92	1.9	10.03
6	mono6_n3_atra	Control, atRA, patient2	17419894	fastqc	17321588	fastqc	0.15	0.0	6.64	2.41	9.2
7	mono6_n5_atra	Control, atRA, patient3	16917763	fastqc	16879615	fastqc	0.35	0.01	12.11	3.35	15.82
8	mono6_n6_atra	Control, atRA, patient4	22023773	fastqc	21979213	fastqc	0.23	0.01	12.27	4.24	16.75
9	mono6_n2_vitd	Control, vitD, patient1	20276337	fastqc	20227638	fastqc	0.31	0.0	8.46	1.84	10.61
10	mono6_n3_vitd	Control, vitD, patient2	17215084	fastqc	17177402	fastqc	0.39	0.01	6.61	1.89	8.9
11	mono6_n5_vitd	Control, vitD, patient3	22390176	fastqc	22333423	fastqc	0.27	0.01	10.48	3.75	14.51
12	mono6_n6_vitd	Control, vitD, patient4	13234576	fastqc	13206378	fastqc	0.36	0.01	11.18	5.25	16.8
13	mono6_n2_asp	A. fumigatus, patient1	18975790	fastqc	18944944	fastqc	0.22	0.0	10.72	2.38	13.32
14	mono6_n3_asp	A. fumigatus, patient2	16997078	fastqc	16962120	fastqc	0.27	0.0	10.77	2.82	13.86
15	mono6_n5_asp	A. fumigatus, patient3	18410955	fastqc	18365497	fastqc	0.28	0.01	13.36	3.74	17.39
16	mono6_n6_asp	A. fumigatus, patient4	16271274	fastqc	16231224	fastqc	0.28	0.01	10.6	3.48	14.37
17	mono6_n2_asp_atra	A. fumigatus, atRA, patient1	21033117	fastqc	21002490	fastqc	0.16	0.0	9.74	2.21	12.11
18	mono6_n3_asp_atra	A. fumigatus, atRA, patient2	15956658	fastqc	15927438	fastqc	0.28	0.0	10.4	3.06	13.74
19	mono6_n5_asp_atra	A. fumigatus, atRA, patient3	21254905	fastqc	21206885	fastqc	0.22	0.0	11.41	3.17	14.8
20	mono6_n6_asp_atra	A. fumigatus, atRA, patient4	20344699	fastqc	20306333	fastqc	0.23	0.01	12.93	3.14	16.31
21	mono6_n2_asp_vitd	A. fumigatus, vitD, patient1	18064825	fastqc	18034506	fastqc	0.18	0.0	8.99	2.3	11.47
22	mono6_n3_asp_vitd	A. fumigatus, vitD, patient2	15134188	fastqc	15107187	fastqc	0.35	0.01	8.33	2.04	10.73
23	mono6_n5_asp_vitd	A. fumigatus, vitD, patient3	20166494	fastqc	20112808	fastqc	0.24	0.0	12.16	4.15	16.55
24	mono6_n6_asp_vitd	A. fumigatus, vitD, patient4	20798344	fastqc	20749414	fastqc	0.2	0.0	13.61	3.85	17.66
25	mono6_n2_can	C. albicans, patient1	19019920	fastqc	18971929	fastqc	0.24	0.0	12.57	2.51	15.32
26	mono6_n3_can	C. albicans, patient2	16133515	fastqc	16090854	fastqc	0.23	0.0	14.06	3.68	17.97
27	mono6_n5_can	C. albicans, patient3	24224699	fastqc	24171173	fastqc	0.29	0.01	16.11	3.98	20.39
28	mono6_n6_can	C. albicans, patient4	13603513	fastqc	13573620	fastqc	0.33	0.0	15.23	3.63	19.19
29	mono6_n2_can_atra	C. albicans, atRA, patient1	16777446	fastqc	16739774	fastqc	0.22	0.0	12.37	2.1	14.69
30	mono6_n3_can_atra	C. albicans, atRA, patient2	14210821	fastqc	14183977	fastqc	0.24	0.0	11.93	3.22	15.39
31	mono6_n5_can_atra	C. albicans, atRA, patient3	20690944	fastqc	20647138	fastqc	0.23	0.0	15.08	3.87	19.18
32	mono6_n6_can_atra	C. albicans, atRA, patient4	12791976	fastqc	12767608	fastqc	0.29	0.01	16.4	4.25	20.95
33	mono6_n2_can_vitd	C. albicans, vitD, patient1	17974044	fastqc	17923308	fastqc	0.24	0.0	10.37	1.85	12.46
34	mono6_n3_can_vitd	C. albicans, vitD, patient2	14005862	fastqc	13975880	fastqc	0.25	0.0	13.9	4.13	18.28
35	mono6_n5_can_vitd	C. albicans, vitD, patient3	24372078	fastqc	24311219	fastqc	0.27	0.0	21.24	5.31	26.82
36	mono6_n6_can_vitd	C. albicans, vitD, patient4	14773802	fastqc	14740105	fastqc	0.29	0.01	15.09	4.4	19.79
37	mono6_n2_eco	E. coli, patient1	18225383	fastqc	18194531	fastqc	0.23	0.0	12.23	2.61	15.07
38	mono6_n3_eco	E. coli, patient2	19427019	fastqc	19381897	fastqc	0.25	0.0	10.33	3.32	13.9
39	mono6_n5_eco	E. coli, patient3	20668435	fastqc	20622966	fastqc	0.29	0.01	10.63	3.31	14.24
40	mono6_n6_eco	E. coli, patient4	13152262	fastqc	13116633	fastqc	0.21	0.01	9.65	3.12	12.99
41	mono6_n2_eco_atra	E. coli, atRA, patient1	17344978	fastqc	17315713	fastqc	0.27	0.0	11.86	3.01	15.14
42	mono6_n3_eco_atra	E. coli, atRA, patient2	18186574	fastqc	18157074	fastqc	0.28	0.0	9.63	3.09	13.0
43	mono6_n5_eco_atra	E. coli, atRA, patient3	19043775	fastqc	19008807	fastqc	0.29	0.0	9.42	2.59	12.3
44	mono6_n6_eco_atra	E. coli, atRA, patient4	14741789	fastqc	14716030	fastqc	0.27	0.01	7.98	2.53	10.79
45	mono6_n2_eco_vitd	E. coli, vitD, patient1	16342360	fastqc	16314916	fastqc	0.3	0.0	9.3	2.31	11.91
46	mono6_n3_eco_vitd	E. coli, vitD, patient2	19787599	fastqc	19745183	fastqc	0.26	0.0	9.33	2.92	12.51
47	mono6_n5_eco_vitd	E. coli, vitD, patient3	18416935	fastqc	18374803	fastqc	0.36	0.01	11.02	2.71	14.1
48	mono6_n6_eco_vitd	E. coli, vitD, patient4	14328322	fastqc	14302232	fastqc	0.32	0.01	14.34	4.39	19.06

S2: Differential gene expression, pairwise DESeq2 comparisons

Shown are certain pairwise DESeq2 comparisons including significant (adjusted p-value < 0.05) protein- and non-coding genes and their expression.

Attention tables include many figures and need some time to be fully loaded. Excel sheets can be downloaded on the sub pages.

Control vs Control atRA	Control vs Control vitD	Control vs A. fumigatus	Control vs C. albicans
Control vs E. coli	Control atRA vs A. fumigatus atRA	Control atRA vs C. albicans atRA	Control atRA vs E. coli atRA
Control vitD vs A. fumigatus vitD	Control vitD vs C. albicans vitD	Control vitD vs E. coli vitD	A. fumigatus vs A. fumigatus atRA
A. fumigatus vs A. fumigatus vitD	C. albicans vs C. albicans atra	C. albicans vs C. albicans vitD	E. coli vs E. coli atra
E. coli vs E. coli vitD

S3: Known ncRNAs related to fungal infections from literature

The table shows ncRNAs related to fungal infections known from literature and how they were significantly expressed (or not) in the data presented here. The column "Position" shows the rank of the ncRNA in the absolute fold change sorted table of all investigated ncRNAs over all pairwise comparisons.

*Example:
ncRNA ANRIL, already known from literature to releated with fungal infections, shows the highest significant expression pattern over all pairwise comparisons. Although, it appears only at position 1996 in the significance sorted list of ncRNA genes.

NcRNAs labeld as N/A were not found in our set of significant differentially expressed genes.

• Download CSV

nr	Name	Box plot	Position*	Expression pattern (foldChange)
01	ANRIL, CDKN2B-AS1		1996	Highest up-regulation in mono6_vitd_mono6_can_vitd (2.2), also up-regulated in mono6_atra_mono6_can_atra (1), mono6ctr_mono6_can (1.4), mono6_ctr_mono6_eco(1.4) and mono6_vitd_mono6_eco_vitd(1.1), BUT down-regulated in mono6_ctr_mono6_asp(-0.8) and, mono6_eco_mono6_eco_atra(-0.8)
02	LET-7A-1, MIRLET7A1		2054	Highest up-regulation in mono6_ctr_mono6_(can,eco) (2.2, 1.7), up-regulated in mono6_vitd_mono6_(asp,can,eco)_vitd (1.2, 1.7, 1), slightly up-regulated in mono6_atra_mono6_(asp,can,eco)_atra (0.5, 1, 1.3)
03	HOTAIRM1		2578	Down-regulated in mono6_atra_mono6_(asp,can,eco)_atra (-1,-1.9,.-2), up-regulated in mono6_ctr_mono6_atra (1.4)
04	NESPAS, GNAS-AS1	NA	2617	Up-regulated in mono6_atra_mono6_(asp,can,eco)_atra (0.8, 1.7, 1.1) and mono6_ctr_mono6_(can,eco) (1.9, 1.2) and mono6_vitd_mono6_can_vitd (1.4), BUT down-regulated in mono6_vitd_mono6_eco_vitd (-1)
05	GTL2-AS (LincRNA MEG3 (GTL2))		2666	Up-regulated in mono6_atra_mono6_(asp,can,eco)_atra (0.9, 1.9, 0.6)
06	HOXA-AS2		3157	Down-regulated in mono_atra_mono6_(asp,eco)_atra (-0.7, -1.7), up- regulated in mono6_ctr_mono6_atra (0.7), BUT down in mono6_ctr_mono6_(can,eco) (-1, -1.1) and down in mono6_vitd_mono6_can_vitd (-1.3)
07	NAMA	NA	3163	Up-regulated in mono6_ctr_mono6_(asp,can) (1.7, 1.6), down-regulated in mono6atra_mono6_(can,eco)_atra (-0.9, 1)
08	NEAT2, MALAT1		3283	Highest up-regulation in mono6_vitd_mono6_infection_vitd (highest with ecoli (1.6)), only slightly differentially expressed in other groups
09	KCNQ1OT1		3342	Highest up-regulation in mono6_vitd_mono6_infection_vitd (highest with ecoli (1.7), slightly down-regulated in mono6_ctr_mono6_(asp,atra,can)
10	HOTTIP	NA	4257	Up-regulated in mono6_atra_mono6_(asp,can,eco)_atra (0.6, 1.4, 1.1) and mono6_vitd_mono6_(asp,eco)_vitd (1.5, 1.3)
11	THRIL	NA	4860	Highest up-regulation in mono6_ctr_mono6_eco(1.3)
12	PCGEM1	NA	5036	Only up-regulated in mono6_atra_mono6_eco_atra (1.3) otherwise not differentially expressed
13	HOXD-AS1, HAGLR	NA	5348	Only up-regulated in mono6_ctr_mono6_eco (1.3)
14	XIST	NA	7285	Lowest expression in mono6_ctr_mono6_eco (-1.2), otherwise not differentially expressed
15	AIRN	NA	10764	Only slightly expressed in mono6_atra_mono6_asp_atra (0.6) and mono6_ctr_mono_6_asp (0.6) (same expression values as most entries in this line regions), otherwise no data
16	HOTAIR	NA	18380	Only N/A
17	MALAT1	NA	18871	Only N/A
18	H19		N/A
19	SRA-1		N/A
20	HOXD13	NA	N/A
21	HOXA11	NA	N/A

S4: Scatter plots of additional comparisons

Significant differential expressed genes are marked red and ncRNAs blue.

	Unstimulated	A. fumigatus	C. albicans	E. coli
atRA
vitD

S5: Box plots and conserved secondary structure: additional ncRNAs as potential marker genes

Shown are expression box plots of ncRNAs that could be used as potential marker genes in different infection and treatment settings.

Visualized are the top candidates for each setting, please click on a thumbnail to open the full PDF. Full sorted candidate lists can be downloaded as tab-separated files (TSV) as well.

Infection specific TSV | PDF	Infection atRA specific TSV | PDF	Infection vitD specific TSV | PDF	Fungi specific TSV | PDF	Vitamin specific TSV | PDF
A. fumigatus specific TSV | PDF	C. albicans specific TSV | PDF	E. coli specific TSV | PDF	atRA specific TSV | PDF	vitD specific TSV | PDF

Conserved substructures of marker genes, using RNAalifold (window wise approach) on UCSC mulitz7 whole genome alignment among Homo sapines (HS), Pan troglodytes (PN), Canis lupus familiaris (CF), Rattus norvegicus (RN), Mus musculus (MM) and Monodelphis domestica (MD)

Infection specific	A. fumigatus specific	C. albicans specific	vitD specific

S6: Antisense and lincRNA heat maps

top 50 most variant antisense RNAs (PDF)	top 50 most variant lincRNAs (PDF)

S7: Pathway heat map of antisense transcripts

Pathway heat map of antisense read counts mapped onto the corresponding sense protein-coding genes as reported in KEGG

S8: Differential expressed isoforms

We investigated differentially expressed isoforms of all ncRNAs by searching for significant differential expressed exons, listed in STab 8.

Gene ID	Gene Name	Gene Biotype	Differentially Expressed Exon	log2 Foldchange	Adjusted p-Value	Comparison
ENSG00000172965	MIR4435-1HG	lincRNA	028	2.39898791396823	0.00023719591868654	mono6_vitd_vs_mono6_can_vitd
ENSG00000172965	MIR4435-1HG	lincRNA	029	2.49380180078702	3.31030574227139e-05	mono6_vitd_vs_mono6_can_vitd
ENSG00000176659	C20orf197	lincRNA	004	-4.47737283084896	1.2769317136546e-10	mono6_vitd_vs_mono6_asp_vitd
ENSG00000177337	DLGAP1-AS1	antisense	009	2.80229521084238	7.41519530858328e-08	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177337	DLGAP1-AS1	antisense	010	3.03340605586852	3.53334803562556e-10	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177406	RP11-218M22.1	antisense	008	-1.07129293826393	0.0330235697861088	mono6_atra_vs_mono6_eco_atra
ENSG00000178977	LINC00324	lincRNA	001	-3.27983463330276	2.01857585599344e-12	mono6_vitd_vs_mono6_eco_vitd
ENSG00000179743	FLJ37453	antisense	001	-1.36971873351646	0.0110025209666268	mono6_vitd_vs_mono6_eco_vitd
ENSG00000185433	LINC00158	lincRNA	001	-2.20446648200565	0.000126272885286207	mono6_eco_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	002	1.07878966755042	0.0135266175387313	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	003	0.981315625837891	0.0127850530893003	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	004	0.916104926194466	0.0170181219625818	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	005	1.45263194879294	0.00876388035975492	mono6_vitd_vs_mono6_asp_vitd
ENSG00000186594	MIR22HG	lincRNA	006	1.3488437391809	0.0148357177188068	mono6_vitd_vs_mono6_asp_vitd
ENSG00000186594	MIR22HG	lincRNA	007	0.956845307104122	0.0248036983285284	mono6_ctr_vs_mono6_eco
ENSG00000186594	MIR22HG	lincRNA	008	1.41368795045608	0.00164084722659317	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	009	1.0777747131838	0.0349687059653099	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	010	1.26014415263512	0.00778539929872839	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	011	1.06740134261299	0.0219322883563084	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	012	1.05567441285944	0.0232024351807044	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	013	1.24386895751517	0.00446557661953216	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	014	1.1268861492923	0.045391770604811	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	015	1.21533539131991	0.0244061780113122	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	016	1.41301027778162	0.00256553640426006	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	017	1.43180671259588	0.00148267875244482	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	018	1.20471377387916	0.00959957979115885	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	019	1.30110641980764	0.00449159978646671	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	020	1.39875551993869	0.00276967515269324	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	021	1.49220451265596	0.000953509777403362	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	022	1.58669026153909	0.000580782256011712	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	023	1.70177812171461	0.000210861862679781	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	024	1.25502155994638	0.00302367573113371	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	025	1.37852871445868	0.0122801717369536	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	026	0.941544945256263	0.0294216519433969	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	027	0.995567699765901	0.0215843763472184	mono6_vitd_vs_mono6_eco_vitd
ENSG00000186594	MIR22HG	lincRNA	031	1.11319619572515	0.0293352902404652	mono6_atra_vs_mono6_asp_atra
ENSG00000203364	RP11-370F5.4	lincRNA	003	7.3882302463525	7.19868767569953e-13	mono6_atra_vs_mono6_can_atra
ENSG00000203644	RP11-332M2.1	sense_intronic	001	-1.18550298967745	0.00428126229024185	mono6_vitd_vs_mono6_can_vitd
ENSG00000203999	LINC01270	lincRNA	006	2.44192074335115	7.04576049628927e-05	mono6_ctr_vs_mono6_vitd
ENSG00000177410	ZFAS1	antisense	007	-5.35204971749839	4.15403627317624e-12	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177410	ZFAS1	antisense	009	-5.21493389938822	3.71603398561392e-13	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177410	ZFAS1	antisense	010	-4.99573294640668	1.02272748128767e-17	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177410	ZFAS1	antisense	011	-4.91698132824029	8.08076345632643e-17	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177410	ZFAS1	antisense	012	-6.03009949530808	6.08166112004215e-23	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177410	ZFAS1	antisense	017	-4.69784284249795	3.44175696635848e-18	mono6_vitd_vs_mono6_eco_vitd
ENSG00000177410	ZFAS1	antisense	020	-1.90465163511037	1.95105735380111e-08	mono6_vitd_vs_mono6_eco_vitd
ENSG00000214894	LINC00243	lincRNA	002	5.80513991402318	5.58008854119014e-09	mono6_vitd_vs_mono6_eco_vitd
ENSG00000215458	AATBC	antisense	001	2.38547826304376	0.01009832059179	mono6_vitd_vs_mono6_asp_vitd
ENSG00000215458	AATBC	antisense	003	-2.46483563531587	6.24626339916647e-07	mono6_ctr_vs_mono6_vitd
ENSG00000215458	AATBC	antisense	004	1.13728361281604	0.00755929546222147	mono6_ctr_vs_mono6_asp
ENSG00000215458	AATBC	antisense	005	1.48393424695002	0.00526276048747005	mono6_ctr_vs_mono6_asp
ENSG00000215458	AATBC	antisense	007	1.12277761088482	0.0111692120162953	mono6_ctr_vs_mono6_asp
ENSG00000215908	CROCCP2	lincRNA	001	-1.50974108104242	0.000330063739936448	mono6_vitd_vs_mono6_eco_vitd
ENSG00000218510	LINC00339	lincRNA	007	-1.32497193208331	0.00437108400282596	mono6_atra_vs_mono6_asp_atra
ENSG00000222041	LINC00152	lincRNA	017	1.71313345386387	0.0115993003618925	mono6_vitd_vs_mono6_eco_vitd
ENSG00000222041	LINC00152	lincRNA	018	2.41244914024656	0.000264801769582618	mono6_vitd_vs_mono6_can_vitd
ENSG00000223387	RP11-408H1.3	lincRNA	004	7.10374617729023	4.40189214021277e-16	mono6_vitd_vs_mono6_can_vitd
ENSG00000223552	RP11-24F11.2	antisense	001	-1.46464359003264	0.0084501044472042	mono6_vitd_vs_mono6_asp_vitd
ENSG00000223969	AC002456.2	antisense	007	3.36352689184292	3.31939156807749e-08	mono6_atra_vs_mono6_asp_atra
ENSG00000224032	EPB41L4A-AS1	lincRNA	005	-3.32339994429738	3.03919847892499e-10	mono6_vitd_vs_mono6_eco_vitd
ENSG00000224152	AC009506.1	antisense	002	-1.09532205835003	0.00804002143169047	mono6_vitd_vs_mono6_eco_vitd
ENSG00000224397	LINC01272	lincRNA	005	-2.26741213582765	4.31026174170235e-05	mono6_vitd_vs_mono6_eco_vitd
ENSG00000224397	LINC01272	lincRNA	006	-1.90999741738492	0.00201694103707573	mono6_vitd_vs_mono6_eco_vitd
ENSG00000224397	LINC01272	lincRNA	007	-2.1881626854853	0.000399063362966249	mono6_vitd_vs_mono6_eco_vitd
ENSG00000224397	LINC01272	lincRNA	008	1.87975988941877	0.000517884428440305	mono6_ctr_vs_mono6_vitd
ENSG00000224397	LINC01272	lincRNA	009	1.55201258046567	0.0049656297133075	mono6_eco_vs_mono6_eco_vitd
ENSG00000224397	LINC01272	lincRNA	010	1.55780281998587	0.00155472505053523	mono6_eco_vs_mono6_eco_vitd
ENSG00000224397	LINC01272	lincRNA	011	1.55420163493559	0.00138253372602142	mono6_eco_vs_mono6_eco_vitd
ENSG00000224397	LINC01272	lincRNA	012	1.40397040469123	0.00521529035897047	mono6_eco_vs_mono6_eco_vitd
ENSG00000224596	ZMIZ1-AS1	antisense	001	3.52706343798892	2.17731926769539e-08	mono6_vitd_vs_mono6_eco_vitd
ENSG00000224596	ZMIZ1-AS1	antisense	004	3.08942819361281	5.24969240273355e-09	mono6_atra_vs_mono6_asp_atra
ENSG00000224596	ZMIZ1-AS1	antisense	006	3.242369940806	3.51200751695969e-14	mono6_atra_vs_mono6_asp_atra
ENSG00000224596	ZMIZ1-AS1	antisense	007	4.97153021859984	2.6685835042328e-22	mono6_atra_vs_mono6_asp_atra
ENSG00000224821	COL4A2-AS2	antisense	005	1.99252706254905	0.0148271073838189	mono6_vitd_vs_mono6_can_vitd
ENSG00000225733	FGD5-AS1	antisense	006	-1.26531906708515	0.00177232254871992	mono6_vitd_vs_mono6_eco_vitd
ENSG00000225733	FGD5-AS1	antisense	008	-1.28041228984695	0.00206321981369849	mono6_vitd_vs_mono6_eco_vitd
ENSG00000225733	FGD5-AS1	antisense	009	-1.05265327205999	0.00498762903128985	mono6_vitd_vs_mono6_eco_vitd
ENSG00000226137	BAIAP2-AS1	lincRNA	001	-1.5489348389233	0.00634388575022133	mono6_ctr_vs_mono6_vitd
ENSG00000226137	BAIAP2-AS1	lincRNA	002	-4.95179037683809	2.87282895454361e-13	mono6_vitd_vs_mono6_eco_vitd
ENSG00000226328	NUP50-AS1	lincRNA	001	1.76328700251282	1.89759900532511e-05	mono6_ctr_vs_mono6_atra
ENSG00000226328	NUP50-AS1	lincRNA	003	1.91284420358204	5.65574960321261e-09	mono6_ctr_vs_mono6_atra
ENSG00000226752	PSMD5-AS1	antisense	043	-1.26607143154596	0.0482141996835409	mono6_ctr_vs_mono6_asp
ENSG00000227039	ITGB2-AS1	antisense	017	-2.64568293226808	6.62503237940453e-06	mono6_vitd_vs_mono6_eco_vitd
ENSG00000227199	ST7-AS1	antisense	001	-1.26199943469395	0.0391454465017982	mono6_can_vs_mono6_can_vitd
ENSG00000228223	HCG11	lincRNA	001	-1.92310978337288	4.38341815082338e-05	mono6_ctr_vs_mono6_asp
ENSG00000228800	RP11-253D19.1	lincRNA	001	9.64044737231519	3.06880018460726e-07	mono6_vitd_vs_mono6_eco_vitd
ENSG00000230438	SERPINB9P1	lincRNA	001	5.24731109108	1.42865443622519e-35	mono6_vitd_vs_mono6_eco_vitd
ENSG00000230438	SERPINB9P1	lincRNA	002	5.25365036326443	9.49786306053833e-34	mono6_vitd_vs_mono6_eco_vitd
ENSG00000230647	AC022816.2	lincRNA	005	7.79423870685319	1.84567079868225e-22	mono6_vitd_vs_mono6_eco_vitd
ENSG00000230844	ZNF674-AS1	lincRNA	004	2.73395016743646	6.60884200572057e-07	mono6_atra_vs_mono6_can_atra
ENSG00000231025	RP11-175O19.4	antisense	001	-1.04282365294123	0.0139953482825671	mono6_vitd_vs_mono6_can_vitd
ENSG00000231721	LINC-PINT	antisense	007	2.7768272900269	6.09875996877775e-06	mono6_ctr_vs_mono6_asp
ENSG00000231721	LINC-PINT	antisense	021	1.83694827135201	0.0222498548117388	mono6_vitd_vs_mono6_asp_vitd
ENSG00000232533	AC093673.5	antisense	001	-1.65215872879327	0.00031588894614275	mono6_vitd_vs_mono6_eco_vitd
ENSG00000232533	AC093673.5	antisense	002	-2.31887215255176	0.000327241966053969	mono6_ctr_vs_mono6_eco
ENSG00000232618	RP11-439L18.1	lincRNA	003	6.17272675673278	4.16531800870862e-12	mono6_vitd_vs_mono6_can_vitd
ENSG00000232956	SNHG15	lincRNA	003	2.50704525586865	5.35742532797582e-07	mono6_ctr_vs_mono6_eco
ENSG00000232956	SNHG15	lincRNA	004	2.44578284276912	1.83661196024255e-07	mono6_ctr_vs_mono6_eco
ENSG00000232956	SNHG15	lincRNA	005	1.9638451451977	4.94410312451502e-10	mono6_ctr_vs_mono6_eco
ENSG00000232956	SNHG15	lincRNA	008	1.58827081285455	0.000105963166008851	mono6_ctr_vs_mono6_eco
ENSG00000232956	SNHG15	lincRNA	009	1.99936953961706	4.96358476082113e-07	mono6_ctr_vs_mono6_eco
ENSG00000233038	AC011899.9	antisense	003	-0.973928120537869	0.0231334399326646	mono6_atra_vs_mono6_asp_atra
ENSG00000233038	AC011899.9	antisense	006	5.79306302118486	1.49539480233239e-22	mono6_ctr_vs_mono6_atra
ENSG00000233038	AC011899.9	antisense	008	5.68477996761201	4.67136957920922e-19	mono6_ctr_vs_mono6_atra
ENSG00000233038	AC011899.9	antisense	009	5.40774734009751	8.42327550950393e-29	mono6_ctr_vs_mono6_atra
ENSG00000233038	AC011899.9	antisense	010	5.43958288424751	6.4163029695369e-33	mono6_ctr_vs_mono6_atra
ENSG00000233058	LINC00884	antisense	001	7.5128366323738	1.20382476823344e-28	mono6_vitd_vs_mono6_eco_vitd
ENSG00000233621	LINC01137	antisense	001	1.40737176401199	0.0260865319779024	mono6_eco_vs_mono6_eco_atra
ENSG00000233705	SLC26A4-AS1	antisense	008	5.95580731236738	9.67431750665897e-13	mono6_eco_vs_mono6_eco_atra
ENSG00000233705	SLC26A4-AS1	antisense	009	3.10177870197407	0.031379340349025	mono6_atra_vs_mono6_eco_atra
ENSG00000234191	RP11-157D23.2	lincRNA	003	-2.12884037850468	0.000126272885286207	mono6_eco_vs_mono6_eco_vitd
ENSG00000234608	MAPKAPK5-AS1	lincRNA	007	-1.78049180552329	0.0275908310034909	mono6_vitd_vs_mono6_asp_vitd
ENSG00000234608	MAPKAPK5-AS1	lincRNA	013	-1.51956411174525	0.0365065465579146	mono6_vitd_vs_mono6_asp_vitd
ENSG00000234608	MAPKAPK5-AS1	lincRNA	016	1.26323501552363	0.018220990689659	mono6_ctr_vs_mono6_vitd
ENSG00000234883	MIR155HG	lincRNA	002	6.90413457668451	2.66102130910731e-12	mono6_vitd_vs_mono6_can_vitd
ENSG00000234883	MIR155HG	lincRNA	003	5.17584502717541	8.21990743952419e-14	mono6_ctr_vs_mono6_eco
ENSG00000234883	MIR155HG	lincRNA	004	7.84877531447775	1.71123839884199e-18	mono6_vitd_vs_mono6_eco_vitd
ENSG00000234883	MIR155HG	lincRNA	005	9.49252637512187	9.49786306053833e-34	mono6_vitd_vs_mono6_eco_vitd
ENSG00000234883	MIR155HG	lincRNA	006	9.47427699535004	1.35916713918633e-67	mono6_vitd_vs_mono6_eco_vitd
ENSG00000235151	AC114730.2	lincRNA	002	6.36778136332352	1.98851322406225e-15	mono6_vitd_vs_mono6_can_vitd
ENSG00000236116	AC064853.2	sense_intronic	001	3.6487250945092	0.00235720014825177	mono6_eco_vs_mono6_eco_atra
ENSG00000236116	AC064853.2	sense_intronic	002	3.98451354312938	0.00243798099295882	mono6_eco_vs_mono6_eco_atra
ENSG00000236352	AC005220.3	antisense	001	7.0106900584941	4.17321880598906e-24	mono6_vitd_vs_mono6_can_vitd
ENSG00000236352	AC005220.3	antisense	003	8.09409907957021	2.27822684733022e-24	mono6_vitd_vs_mono6_can_vitd
ENSG00000236700	LINC01010	lincRNA	006	5.18792897626211	2.92315163249944e-06	mono6_vitd_vs_mono6_asp_vitd
ENSG00000237181	AC147651.4	antisense	001	4.65294790396244	6.97595770113461e-15	mono6_vitd_vs_mono6_eco_vitd
ENSG00000237181	AC147651.4	antisense	002	4.66703744415919	1.64063712321227e-21	mono6_vitd_vs_mono6_eco_vitd
ENSG00000237513	RP11-325F22.2	lincRNA	001	6.82344952454871	1.20382476823344e-28	mono6_vitd_vs_mono6_eco_vitd
ENSG00000237513	RP11-325F22.2	lincRNA	002	7.41716766983816	2.07744582684408e-44	mono6_vitd_vs_mono6_eco_vitd
ENSG00000237513	RP11-325F22.2	lincRNA	004	5.90469330238473	7.42996904936166e-16	mono6_vitd_vs_mono6_eco_vitd
ENSG00000237513	RP11-325F22.2	lincRNA	005	6.69309900307651	2.84816107912479e-25	mono6_vitd_vs_mono6_eco_vitd
ENSG00000238033	AC002480.2	lincRNA	001	9.76285806282623	6.42550042961677e-08	mono6_vitd_vs_mono6_can_vitd
ENSG00000240859	AC093627.10	lincRNA	008	3.71531598816986	2.44877356932779e-11	mono6_ctr_vs_mono6_atra
ENSG00000240859	AC093627.10	lincRNA	009	3.55458028907797	7.53301023787684e-18	mono6_ctr_vs_mono6_atra
ENSG00000240859	AC093627.10	lincRNA	010	4.21020453683413	2.03427077963191e-21	mono6_ctr_vs_mono6_atra
ENSG00000240859	AC093627.10	lincRNA	011	-7.23126809354441	2.17447360784342e-12	mono6_vitd_vs_mono6_eco_vitd
ENSG00000241280	RP11-221J22.2	lincRNA	009	3.64007153671682	1.00521608718682e-06	mono6_atra_vs_mono6_can_atra
ENSG00000244567	AC096772.6	lincRNA	001	3.06830818060276	5.31026326057345e-05	mono6_vitd_vs_mono6_asp_vitd
ENSG00000244567	AC096772.6	lincRNA	002	3.19240208278042	0.000417217181275778	mono6_vitd_vs_mono6_asp_vitd
ENSG00000245060	LINC00847	lincRNA	010	0.954425357195707	0.0493504181323251	mono6_vitd_vs_mono6_can_vitd
ENSG00000245060	LINC00847	lincRNA	011	1.36636417755614	0.004478860373708	mono6_ctr_vs_mono6_atra
ENSG00000245060	LINC00847	lincRNA	012	1.45248455254533	0.0169984040416116	mono6_vitd_vs_mono6_asp_vitd
ENSG00000246100	LINC00900	lincRNA	001	2.8522525088942	2.42095756499146e-15	mono6_ctr_vs_mono6_atra
ENSG00000247271	ZBED5-AS1	antisense	006	-2.7089631363345	5.90377650645954e-08	mono6_ctr_vs_mono6_eco
ENSG00000247982	LINC00926	lincRNA	001	3.08944958642437	1.0770018692398e-06	mono6_vitd_vs_mono6_eco_vitd
ENSG00000247982	LINC00926	lincRNA	003	4.78010011134513	1.01901104464028e-13	mono6_vitd_vs_mono6_eco_vitd
ENSG00000247982	LINC00926	lincRNA	004	3.59397269387359	2.17447360784342e-12	mono6_vitd_vs_mono6_eco_vitd
ENSG00000248008	NRAV	antisense	001	-1.25033550319517	0.0228271730885348	mono6_asp_vs_mono6_asp_atra
ENSG00000248323	LUCAT1	lincRNA	001	2.8723394932935	5.60789906278203e-09	mono6_vitd_vs_mono6_eco_vitd
ENSG00000248323	LUCAT1	lincRNA	003	3.06952411938217	2.25707197668421e-13	mono6_vitd_vs_mono6_eco_vitd
ENSG00000248323	LUCAT1	lincRNA	004	2.60731830753058	3.71571708179005e-10	mono6_vitd_vs_mono6_eco_vitd
ENSG00000248323	LUCAT1	lincRNA	005	2.70041826513461	4.54807021606428e-06	mono6_vitd_vs_mono6_eco_vitd
ENSG00000248323	LUCAT1	lincRNA	007	2.43201507448456	5.63869905517795e-10	mono6_vitd_vs_mono6_eco_vitd
ENSG00000248323	LUCAT1	lincRNA	009	1.82081740215614	5.33631673076355e-05	mono6_vitd_vs_mono6_eco_vitd
ENSG00000248323	LUCAT1	lincRNA	010	2.20234592540296	2.15657094273419e-05	mono6_vitd_vs_mono6_eco_vitd
ENSG00000250274	CTB-114C7.4	lincRNA	001	5.56166191067306	1.71484481274338e-36	mono6_vitd_vs_mono6_eco_vitd
ENSG00000250548	RP11-47I22.2	lincRNA	003	3.01522667765748	4.47367098512335e-07	mono6_vitd_vs_mono6_eco_vitd
ENSG00000250742	RP11-834C11.4	lincRNA	002	1.8060230867191	0.00126287467961356	mono6_vitd_vs_mono6_eco_vitd
ENSG00000250929	LINC01181	antisense	002	-1.87083433953368	0.00459635617084828	mono6_eco_vs_mono6_eco_atra
ENSG00000251230	RP11-701P16.5	lincRNA	001	6.8254894534116	8.13852963056858e-51	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251230	RP11-701P16.5	lincRNA	002	6.70223503357032	4.20632917763032e-56	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251230	RP11-701P16.5	lincRNA	003	5.57607551364697	8.73866520430001e-28	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251230	RP11-701P16.5	lincRNA	004	6.45315581561611	2.67274626584515e-61	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251230	RP11-701P16.5	lincRNA	005	5.76088528810392	3.53248546626695e-18	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251442	LINC01094	lincRNA	013	-3.83511972474962	7.35476661705894e-11	mono6_vitd_vs_mono6_can_vitd
ENSG00000251442	LINC01094	lincRNA	014	-5.79314540344672	5.88432759060305e-27	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251615	RP11-774O3.3	lincRNA	001	2.8815797769135	1.48599378134332e-05	mono6_atra_vs_mono6_can_atra
ENSG00000253522	CTC-231O11.1	lincRNA	001	6.16382688705982	5.97170169714159e-26	mono6_vitd_vs_mono6_can_vitd
ENSG00000253522	CTC-231O11.1	lincRNA	002	6.35523969155573	1.27142311515396e-18	mono6_vitd_vs_mono6_can_vitd
ENSG00000253522	CTC-231O11.1	lincRNA	003	3.9754428919571	3.87194398899509e-14	mono6_vitd_vs_mono6_eco_vitd
ENSG00000253522	CTC-231O11.1	lincRNA	004	4.59761193083585	3.7845263220923e-20	mono6_vitd_vs_mono6_eco_vitd
ENSG00000253593	RP11-157E21.1	lincRNA	002	3.48371336388049	1.35831830470921e-15	mono6_atra_vs_mono6_eco_atra
ENSG00000253738	OTUD6B-AS1	antisense	002	-1.34104172455675	0.00456783038528178	mono6_vitd_vs_mono6_eco_vitd
ENSG00000253738	OTUD6B-AS1	antisense	003	-0.904970902574967	0.0421403960066402	mono6_ctr_vs_mono6_asp
ENSG00000253982	CTD-2336O2.1	antisense	002	1.15466099467892	0.0103386728309399	mono6_atra_vs_mono6_asp_atra
ENSG00000253982	CTD-2336O2.1	antisense	003	-1.71938439021186	0.012757886126359	mono6_vitd_vs_mono6_eco_vitd
ENSG00000254102	RP11-21C4.1	antisense	002	9.62264858656966	1.32761593277489e-07	mono6_ctr_vs_mono6_can
ENSG00000254281	KB-1507C5.4	lincRNA	002	2.65263165136454	0.00111753276393455	mono6_ctr_vs_mono6_eco
ENSG00000254281	KB-1507C5.4	lincRNA	004	3.77295848155798	1.31023748852578e-14	mono6_vitd_vs_mono6_eco_vitd
ENSG00000254528	RP11-728F11.4	antisense	005	-2.89230079598547	4.61225362731926e-07	mono6_vitd_vs_mono6_eco_vitd
ENSG00000254528	RP11-728F11.4	antisense	006	3.01529449673681	0.000109341296575402	mono6_ctr_vs_mono6_can
ENSG00000254635	WAC-AS1	antisense	002	-1.337478065593	0.00177232254871992	mono6_vitd_vs_mono6_eco_vitd
ENSG00000255197	RP11-750H9.5	antisense	001	-3.48559504926701	1.21335205293878e-11	mono6_vitd_vs_mono6_eco_vitd
ENSG00000255197	RP11-750H9.5	antisense	002	-3.3506908604184	2.87282895454361e-13	mono6_vitd_vs_mono6_eco_vitd
ENSG00000255197	RP11-750H9.5	antisense	003	-3.94722306035165	1.49493682151176e-19	mono6_vitd_vs_mono6_eco_vitd
ENSG00000255197	RP11-750H9.5	antisense	004	-5.12231260980988	4.77916070321934e-15	mono6_vitd_vs_mono6_eco_vitd
ENSG00000255521	RP4-607I7.1	antisense	001	8.04139784915878	1.91098983509878e-13	mono6_vitd_vs_mono6_can_vitd
ENSG00000255521	RP4-607I7.1	antisense	002	9.53755819297122	1.71408334417979e-07	mono6_vitd_vs_mono6_can_vitd
ENSG00000255521	RP4-607I7.1	antisense	003	8.96934415513722	7.98159383504654e-13	mono6_vitd_vs_mono6_can_vitd
ENSG00000255874	LINC00346	lincRNA	001	5.50152064548073	3.03675545115405e-11	mono6_vitd_vs_mono6_eco_vitd
ENSG00000255921	RP11-662I13.2	antisense	003	9.43548530550393	3.12894913242119e-07	mono6_vitd_vs_mono6_can_vitd
ENSG00000255921	RP11-662I13.2	antisense	004	6.96241736655126	3.3046986850527e-14	mono6_vitd_vs_mono6_can_vitd
ENSG00000256537	SMIM10L1	lincRNA	002	-1.06858702080236	0.0154599968665909	mono6_vitd_vs_mono6_can_vitd
ENSG00000257027	RP11-705C15.3	sense_intronic	002	2.39426548015664	3.44632502302693e-07	mono6_vitd_vs_mono6_can_vitd
ENSG00000257605	RP11-680A11.5	antisense	001	3.05449879831964	0.00103120901326899	mono6_vitd_vs_mono6_asp_vitd
ENSG00000257605	RP11-680A11.5	antisense	002	4.10170817097154	1.919423065734e-06	mono6_vitd_vs_mono6_asp_vitd
ENSG00000258056	RP11-644F5.11	antisense	002	-1.44567754236908	0.000735903348342473	mono6_vitd_vs_mono6_eco_vitd
ENSG00000258738	RP11-73E17.2	antisense	001	0.89404084110909	0.0349506465736913	mono6_vitd_vs_mono6_eco_vitd
ENSG00000259330	INAFM2	antisense	001	-2.32244939661494	9.27206912857281e-07	mono6_vitd_vs_mono6_can_vitd
ENSG00000259330	INAFM2	antisense	002	-2.69882529951089	7.16151909214773e-12	mono6_vitd_vs_mono6_can_vitd
ENSG00000259436	CTC-378H22.2	antisense	002	-1.36790674059612	0.0115115031349232	mono6_ctr_vs_mono6_vitd
ENSG00000259642	ST20-AS1	antisense	002	1.58276310387027	0.000406799910827725	mono6_eco_vs_mono6_eco_atra
ENSG00000259834	RP11-284N8.3	lincRNA	001	2.71975937330001	4.08410077577276e-07	mono6_vitd_vs_mono6_eco_vitd
ENSG00000259863	SH3RF3-AS1	lincRNA	001	3.24112470020235	3.07196670599033e-08	mono6_atra_vs_mono6_asp_atra
ENSG00000260135	RP11-212I21.2	lincRNA	004	1.60804864965922	0.0255899738756701	mono6_atra_vs_mono6_can_atra
ENSG00000260196	RP1-239B22.5	antisense	001	2.23815366661117	1.03972046235352e-09	mono6_vitd_vs_mono6_eco_vitd
ENSG00000260219	RP11-347C12.10	lincRNA	002	1.48309139347372	0.00711205704946679	mono6_vitd_vs_mono6_can_vitd
ENSG00000260231	JHDM1D-AS1	antisense	001	3.55839089261291	8.90791706783573e-16	mono6_vitd_vs_mono6_eco_vitd
ENSG00000260267	RP11-452L6.5	antisense	001	1.30860582252489	0.00190144575793024	mono6_ctr_vs_mono6_eco
ENSG00000260898	ADPGK-AS1	antisense	001	2.91621073897929	1.23246631069353e-15	mono6_vitd_vs_mono6_can_vitd
ENSG00000261455	LINC01003	lincRNA	001	-1.5630692227433	0.0001560916728876	mono6_atra_vs_mono6_eco_atra
ENSG00000261618	RP11-79H23.3	lincRNA	001	11.4777659114753	7.46225320243037e-51	mono6_vitd_vs_mono6_eco_vitd
ENSG00000261888	AC144831.1	lincRNA	001	1.20808386834048	0.00196448829659361	mono6_vitd_vs_mono6_eco_vitd
ENSG00000263753	LINC00667	lincRNA	017	-1.01296362390084	0.00985928704284372	mono6_ctr_vs_mono6_eco
ENSG00000263823	RP11-326K13.4	antisense	001	1.1178051175403	0.036111461101541	mono6_ctr_vs_mono6_asp
ENSG00000265206	RP5-1171I10.5	antisense	003	0.992311716014087	0.0315236969863308	mono6_vitd_vs_mono6_can_vitd
ENSG00000265494	RP11-131K5.2	lincRNA	001	10.1408868931077	8.59947852191174e-09	mono6_vitd_vs_mono6_can_vitd
ENSG00000265666	RARA-AS1	antisense	001	2.94911116964374	2.2107117557187e-08	mono6_eco_vs_mono6_eco_atra
ENSG00000265975	CTB-41I6.2	lincRNA	001	1.50783370555381	0.00066472188140625	mono6_vitd_vs_mono6_eco_vitd
ENSG00000266389	CTB-41I6.1	lincRNA	002	1.43475681689917	0.000202004917573893	mono6_vitd_vs_mono6_can_vitd
ENSG00000266709	RP11-214O1.2	lincRNA	001	2.53757569412164	2.08326206172933e-05	mono6_vitd_vs_mono6_eco_vitd
ENSG00000266750	MIR4645	miRNA	001	4.90511491766514	7.53232582241463e-17	mono6_vitd_vs_mono6_eco_vitd
ENSG00000266947	RP11-799D4.4	antisense	004	2.81506398595532	9.48227170055684e-10	mono6_atra_vs_mono6_can_atra
ENSG00000266962	RP11-400F19.6	antisense	001	-1.22522342855699	0.0151576307010627	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267034	RP11-384O8.1	lincRNA	001	6.8372205073182	1.288845946519e-29	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267100	ILF3-AS1	lincRNA	001	-2.33647993516497	6.32498966182919e-08	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267121	CTD-2020K17.1	antisense	002	-1.319448171587	0.0196195587857572	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267121	CTD-2020K17.1	antisense	003	-0.934141165728224	0.0212321994322245	mono6_ctr_vs_mono6_can
ENSG00000267121	CTD-2020K17.1	antisense	007	-2.17513330641716	1.19207437414622e-06	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267121	CTD-2020K17.1	antisense	009	-1.36980778741418	0.00157582548550471	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267257	RP11-1151B14.4	antisense	002	-1.51055851524591	0.0186983400680265	mono6_can_vs_mono6_can_vitd
ENSG00000267317	CTB-25B13.12	antisense	001	-0.847929340612726	0.0472701063999344	mono6_atra_vs_mono6_can_atra
ENSG00000267365	KCNJ2-AS1	antisense	001	3.87608760714196	1.17918742071471e-12	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267416	CTD-2319I12.2	lincRNA	002	3.89197237936582	6.68569944012354e-10	mono6_atra_vs_mono6_eco_atra
ENSG00000267519	CTD-3252C9.4	lincRNA	001	2.02110238691852	2.28994334599394e-05	mono6_vitd_vs_mono6_eco_vitd
ENSG00000267737	AC061992.2	lincRNA	003	6.27377084898053	3.48934102482564e-18	mono6_vitd_vs_mono6_eco_vitd
ENSG00000268001	CARD8-AS1	antisense	002	-1.03367545813269	0.00805997754927425	mono6_vitd_vs_mono6_eco_vitd
ENSG00000268205	CTC-444N24.11	lincRNA	001	-1.55394736190713	0.0012951763195259	mono6_vitd_vs_mono6_can_vitd
ENSG00000268734	CTB-61M7.2	lincRNA	001	0.868053571589694	0.0403058344969571	mono6_eco_vs_mono6_eco_atra
ENSG00000268858	RP4-591C20.9	antisense	001	1.61406426228435	1.5960874069246e-05	mono6_vitd_vs_mono6_can_vitd
ENSG00000268895	A1BG-AS1	antisense	017	-0.885893429630869	0.0357821187034184	mono6_ctr_vs_mono6_asp
ENSG00000269220	LINC00528	lincRNA	001	1.02875813200608	0.016420990666143	mono6_vitd_vs_mono6_eco_vitd
ENSG00000269940	RP11-73M18.7	sense_intronic	001	0.982535057726357	0.0291094941467474	mono6_vitd_vs_mono6_eco_vitd
ENSG00000269958	RP11-73M18.8	sense_intronic	001	0.895182121649942	0.041040873987802	mono6_vitd_vs_mono6_eco_vitd
ENSG00000270055	CTD-3092A11.2	sense_intronic	001	1.15188697208788	0.0174582086937545	mono6_atra_vs_mono6_asp_atra
ENSG00000270069	MIR222HG	lincRNA	001	7.04713127132049	7.96335378507513e-19	mono6_vitd_vs_mono6_can_vitd
ENSG00000270170	NCBP2-AS2	lincRNA	001	-2.84133247676689	3.71571708179005e-10	mono6_vitd_vs_mono6_eco_vitd
ENSG00000270574	RP11-171I2.2	antisense	001	1.94859732813672	3.81447586888146e-06	mono6_vitd_vs_mono6_can_vitd
ENSG00000237298	TTN-AS1	antisense	011	1.84309123888651	9.83196541462711e-06	mono6_atra_vs_mono6_can_atra
ENSG00000237298	TTN-AS1	antisense	055	1.43930920395079	0.00442050625663645	mono6_vitd_vs_mono6_can_vitd
ENSG00000237298	TTN-AS1	antisense	058	1.25928302942028	0.00504256799615916	mono6_vitd_vs_mono6_can_vitd
ENSG00000237298	TTN-AS1	antisense	070	3.30291913513377	9.48227170055684e-10	mono6_atra_vs_mono6_can_atra
ENSG00000237298	TTN-AS1	antisense	071	2.43216655931757	5.53737504643557e-09	mono6_vitd_vs_mono6_can_vitd
ENSG00000271011	RP11-171I2.5	antisense	001	3.20217338542367	9.8251352241194e-13	mono6_atra_vs_mono6_can_atra
ENSG00000271122	RP11-379H18.1	antisense	001	-1.18711610239444	0.00980728336733812	mono6_atra_vs_mono6_can_atra
ENSG00000271430	RP3-368A4.5	sense_intronic	001	-1.02178921978715	0.0435230804917835	mono6_atra_vs_mono6_can_atra
ENSG00000271614	LINC00936	lincRNA	001	1.72453594411908	6.49541609664297e-05	mono6_vitd_vs_mono6_can_vitd
ENSG00000271646	RP11-326I11.3	lincRNA	001	1.43665967245828	0.00322739757558114	mono6_vitd_vs_mono6_eco_vitd
ENSG00000271856	LINC01215	lincRNA	003	3.57014011583385	1.35402068589285e-07	mono6_vitd_vs_mono6_eco_vitd
ENSG00000272449	RP3-395M20.12	lincRNA	001	2.3547235052528	0.00765650547134123	mono6_vitd_vs_mono6_asp_vitd
ENSG00000272482	RP11-474O21.5	lincRNA	001	-1.10260312392686	0.0414528954299049	mono6_atra_vs_mono6_eco_atra
ENSG00000272555	RP11-459I19.1	lincRNA	001	2.03461647835246	0.0054209577949552	mono6_ctr_vs_mono6_atra
ENSG00000272625	RP11-737O24.5	antisense	001	2.44225079654625	7.73904085449485e-08	mono6_vitd_vs_mono6_eco_vitd
ENSG00000272669	RP3-508I15.21	antisense	001	3.68529996839449	1.92732893853345e-16	mono6_vitd_vs_mono6_eco_vitd
ENSG00000272686	RP11-390E23.6	antisense	001	1.16945648860792	0.00134271490992763	mono6_vitd_vs_mono6_can_vitd
ENSG00000272825	LL21NC02-1C16.2	antisense	001	-1.52798926727502	0.0206798220865051	mono6_ctr_vs_mono6_vitd
ENSG00000272839	RP11-452C13.1	antisense	001	6.66340435686234	3.98041958561679e-23	mono6_ctr_vs_mono6_atra
ENSG00000272908	RP11-121A8.1	lincRNA	001	1.87386241286763	0.00408661209560371	mono6_atra_vs_mono6_eco_atra
ENSG00000272941	RP11-134L10.1	antisense	001	2.43978921316971	1.38662884835044e-06	mono6_vitd_vs_mono6_eco_vitd
ENSG00000273015	RP11-352M15.2	lincRNA	001	-1.57298269419266	0.00212818046727661	mono6_vitd_vs_mono6_eco_vitd
ENSG00000273033	RP11-67L2.2	lincRNA	001	-3.4158541157264	1.8974327201827e-20	mono6_vitd_vs_mono6_eco_vitd
ENSG00000273117	AC144652.1	lincRNA	001	1.04924979358868	0.0155282620365806	mono6_ctr_vs_mono6_eco
ENSG00000273124	RP11-236B18.5	lincRNA	001	-1.61782110696327	0.0304336119550423	mono6_eco_vs_mono6_eco_vitd
ENSG00000273151	RP11-449P15.2	antisense	001	-1.38567050250907	0.0271564621886412	mono6_ctr_vs_mono6_vitd
ENSG00000273174	RP11-434H6.6	antisense	001	1.21537440093664	0.00334559416916496	mono6_vitd_vs_mono6_eco_vitd
ENSG00000273270	RP11-212P7.2	lincRNA	001	-1.39073382742173	0.000247115303972064	mono6_ctr_vs_mono6_eco
ENSG00000273314	RP5-1136G13.2	antisense	001	2.43409872697219	5.42865525757011e-05	mono6_vitd_vs_mono6_can_vitd
ENSG00000273320	RP11-22N19.2	antisense	001	-1.2014039950117	0.0277651585077395	mono6_eco_vs_mono6_eco_atra
ENSG00000274012	RN7SL2	misc_RNA	001	1.2996623085759	0.0325400032393521	mono6_atra_vs_mono6_eco_atra
ENSG00000251562	MALAT1	lincRNA	007	1.20355225654502	0.00517856856547652	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	008	1.11943665291247	0.0136345411503045	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	009	1.15166508106295	0.0168021773647668	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	014	-1.24913867921593	0.0407598886541549	mono6_ctr_vs_mono6_can
ENSG00000251562	MALAT1	lincRNA	015	1.05641371414642	0.0227923764890089	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	016	1.11911818942607	0.0392477486582367	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	017	1.14729824017842	0.0305972688719562	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	018	1.03667449497444	0.0297605974370407	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	019	0.996348747562426	0.0391187696101103	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	020	-1.07268066115308	0.0262569499581205	mono6_asp_vs_mono6_asp_atra
ENSG00000251562	MALAT1	lincRNA	021	1.27414664849479	0.0331315746961826	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	022	1.37987626137708	0.0150159465598815	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	023	1.1933728168348	0.0416791098828321	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	025	1.10440551623181	0.0415668475476424	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	031	1.26890889999069	0.0353537834849078	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	032	1.29900292830031	0.0404467979841331	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	033	1.26335366865987	0.0457710111228704	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	034	1.27186408621135	0.0307484424764604	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	038	1.26023318108418	0.0494849674302447	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	039	1.42822211527309	0.0175119319661532	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	040	1.53261044324233	0.00950904905433804	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	041	1.71951699971085	0.00809001152740543	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	042	1.84060202719303	0.00247080596862252	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	043	1.81253489101847	0.00265269916385247	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	044	1.5125657810265	0.0289810700969667	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	045	1.64204061316943	0.0155721383352143	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	046	1.3067793057188	0.0353537834849078	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	047	1.21963983394619	0.0410024146183211	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	048	1.20326333663145	0.0482936276460725	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	050	1.25759926983405	0.0392477486582367	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	051	1.24752990548006	0.0215843763472184	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	052	-1.30143985252013	0.0157963096831535	mono6_asp_vs_mono6_asp_atra
ENSG00000251562	MALAT1	lincRNA	053	-1.21260175630007	0.0120438735490318	mono6_asp_vs_mono6_asp_atra
ENSG00000251562	MALAT1	lincRNA	054	1.12578344174517	0.0389243030036814	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	055	1.23119067655764	0.0248031588894258	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	056	1.22155556904299	0.0282527664360438	mono6_vitd_vs_mono6_eco_vitd
ENSG00000251562	MALAT1	lincRNA	057	1.42788747914625	0.0249564537286296	mono6_vitd_vs_mono6_eco_vitd
ENSG00000274213	RP11-670E13.6	lincRNA	001	2.92604772869289	3.84597514887397e-07	mono6_atra_vs_mono6_asp_atra
ENSG00000274215	CTD-2313J17.6	lincRNA	001	4.02818408396929	6.05462346303001e-15	mono6_ctr_vs_mono6_can
ENSG00000226380	AC058791.1	lincRNA	003	6.05335768441947	1.60793689772022e-23	mono6_vitd_vs_mono6_eco_vitd
ENSG00000226380	AC058791.1	lincRNA	005	7.17207160157514	1.25377841789557e-48	mono6_vitd_vs_mono6_eco_vitd
ENSG00000226380	AC058791.1	lincRNA	006	6.816667601835	8.92746903632304e-34	mono6_vitd_vs_mono6_eco_vitd
ENSG00000226380	AC058791.1	lincRNA	007	6.45708801860174	2.23502726324536e-35	mono6_vitd_vs_mono6_eco_vitd
ENSG00000274307	RP11-345J18.2	sense_intronic	001	1.74023361134879	8.46765997262227e-05	mono6_ctr_vs_mono6_can
ENSG00000274383	CTD-2017F17.2	antisense	001	-1.07961703164289	0.0345001182855763	mono6_ctr_vs_mono6_vitd
ENSG00000274536	RP6-159A1.4	antisense	001	2.09233981337461	0.000177083631860044	mono6_ctr_vs_mono6_atra
ENSG00000274536	RP6-159A1.4	antisense	002	2.1923885348199	4.06244315845915e-07	mono6_ctr_vs_mono6_atra
ENSG00000274536	RP6-159A1.4	antisense	003	2.17011963519129	5.38871553966704e-05	mono6_ctr_vs_mono6_atra
ENSG00000274536	RP6-159A1.4	antisense	004	2.34709153802426	1.33831691385354e-06	mono6_ctr_vs_mono6_atra
ENSG00000274536	RP6-159A1.4	antisense	005	-2.6541705067088	0.000213575055029694	mono6_vitd_vs_mono6_eco_vitd
ENSG00000274712	RP11-147L13.15	lincRNA	001	2.07547849739386	0.0356495389854042	mono6_vitd_vs_mono6_asp_vitd
ENSG00000203709	C1orf132	lincRNA	005	2.5336137689121	4.40208450029446e-09	mono6_vitd_vs_mono6_can_vitd
ENSG00000269893	SNHG8	lincRNA	011	-5.74618561006317	1.3157847966172e-11	mono6_vitd_vs_mono6_eco_vitd
ENSG00000269893	SNHG8	lincRNA	012	-1.70066418886758	0.00697844939583564	mono6_vitd_vs_mono6_eco_vitd
ENSG00000253352	TUG1	antisense	023	-1.39904108695874	0.0254615127209661	mono6_atra_vs_mono6_eco_atra
ENSG00000253352	TUG1	antisense	026	-1.55098143227814	0.00537245972474434	mono6_atra_vs_mono6_asp_atra
ENSG00000276107	CTD-2033D15.2	sense_intronic	001	1.27354050195952	0.0157886936217389	mono6_ctr_vs_mono6_eco
ENSG00000233429	HOTAIRM1	antisense	017	1.10718883237057	0.027309529311926	mono6_ctr_vs_mono6_atra
ENSG00000233429	HOTAIRM1	antisense	019	0.959215191260009	0.0415788417739694	mono6_ctr_vs_mono6_atra
ENSG00000276649	RP5-858L17.1	antisense	006	1.30020364246719	0.00465747202291848	mono6_vitd_vs_mono6_can_vitd
ENSG00000276900	RP11-467L13.7	antisense	001	1.37651398069677	0.0184065036045078	mono6_vitd_vs_mono6_can_vitd
ENSG00000276980	CTD-3128G10.7	sense_intronic	001	2.45600652231784	1.21968516090285e-05	mono6_vitd_vs_mono6_eco_vitd
ENSG00000277496	RP11-93B14.9	antisense	001	3.56945009919766	1.26336678402669e-15	mono6_vitd_vs_mono6_eco_vitd
ENSG00000277969	CTB-58E17.1	lincRNA	001	2.30840945696837	6.71745647290016e-09	mono6_vitd_vs_mono6_eco_vitd
ENSG00000278095	RP11-283G6.6	antisense	001	1.47220883349527	0.000919666772380346	mono6_can_vs_mono6_can_vitd
ENSG00000245532	NEAT1	lincRNA	003	2.01245874760149	0.000990699768738156	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	004	2.17886872078631	0.000678502662771783	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	005	1.97823986891869	0.00286337249609061	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	006	1.84765541418448	0.00361203761311857	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	007	1.95192675607024	0.000887165680821441	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	008	1.74331778676619	0.00321866843771333	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	009	1.69065324243572	0.00447758964089638	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	010	1.76801440439156	0.000580782256011712	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	011	2.1036041379952	4.11129241370096e-05	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	012	2.10101934458417	0.000110481966869824	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	013	1.99418778412499	0.000100318844770857	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	014	1.78426315981321	0.000574886652713055	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	015	1.6552203390877	0.00313604485843532	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	016	1.83202060072671	0.000338113703773666	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	017	1.73586801119472	0.000367198963866905	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	018	1.83000727113039	0.00028570381471817	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	019	1.99790180503735	0.00446557661953216	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	020	1.78761631995076	0.0140481921370614	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	021	1.79155446583648	0.015379502673129	mono6_vitd_vs_mono6_eco_vitd
ENSG00000245532	NEAT1	lincRNA	022	1.56280550111727	0.0338175743043752	mono6_vitd_vs_mono6_eco_vitd
ENSG00000278600	RP11-81A1.6	sense_intronic	001	2.33332702141115	7.78693108899515e-10	mono6_ctr_vs_mono6_atra
ENSG00000278730	RP11-147L13.11	lincRNA	001	-1.00717252292247	0.00738551137142336	mono6_vitd_vs_mono6_eco_vitd
ENSG00000278869	CITF22-49E9.3	lincRNA	001	3.22168645490707	4.17330420672721e-08	mono6_ctr_vs_mono6_eco
ENSG00000280798	LINC00294	lincRNA	001	-1.97063126791214	0.000187399364510804	mono6_vitd_vs_mono6_eco_vitd
ENSG00000281183	NPTN-IT1	sense_intronic	001	3.13515768060097	5.15289653835081e-09	mono6_vitd_vs_mono6_eco_vitd

S9: Comparison of different filter parameters

Total and significant differentially expressed number of ncRNAs and proteins based on all pairwise sample comparisons. Variances were calculated over all 48 samples.

approach	0	1	2	3	4	5	6	7	8	9	10	11
filters
p-value $<$	--	--	1	1	1	0.05	0.05	0.05	0.05	--	--	--
$abs(log_2(fc))>$	--	--	0	2	2	0	0	2	2	--	--	--
basemean $>$	--	1	10	0	10	0	10	0	10	--	--	--
variance $>$	--	--	--	--	--	--	--	--	--	0.5	1	2
ncRNA classes
antisense	5561	1474	544	940	264	715	417	568	264	291	118	30
lincRNA	7650	1457	546	1089	321	802	430	696	321	394	177	62
miRNA	4198	137	21	102	11	52	17	44	11	8	6	2
rRNA	549	2	0	3	0	0	0	0	0	0	0	0
scaRNA	49	4	0	2	0	2	0	0	0	0	0	0
sense (intronic)	919	297	74	183	34	111	55	90	34	41	10	3
snoRNA	961	57	8	34	6	15	6	15	6	7	3	0
snRNA	1905	51	4	41	4	14	4	14	4	7	1	0
3' overlapping ncRNA	29	7	3	6	2	3	2	3	2	1	1	0
misc RNA	2306	123	14	91	7	43	14	36	7	12	2	0
total
	24150	3610	1214	2491	649	1757	945	1466	649	761	318	97
proteins
	19825	14931	12436	6589	4738	12414	11487	5689	4738	4038	1756	602

S10: Response element (RARE, VDRE) enrichment

We performed genome-wide in silico analysis of consensus retinoic acid response element (RARE), DR1 and DR5 and vitamin D response element (VDRE) motifs in potential enhancer regions, located upstream and downstream of transcription start sites. RNAbob v2.2 was used to detect the known consensus motif RRGKTCAnnRRGKTCA for VDRE and D5 motif RGKTSAnnnnnRGKTSA for RARE (in IUPAC code). The enrichment was calculated between significant differential expressed and non-significant differential, but expressed lncRNAs using Fisher's exact test. PDF