Identification of protein-coding and non-coding RNA expression profiles in CD34+and in stromal cells in refractory anemia with ringed sideroblasts

Baratti, Mariana O; Moreira, Yuri B; Traina, Fabiola; Costa, Fernando F; Verjovski-Almeida, Sergio; Olalla-Saad, Sara T

doi:10.1186/1755-8794-3-30

Table 3 ncRNAs with significantly altered CD34⁺ expression in MDS-RARS patients in relation to healthy individuals.

From: Identification of protein-coding and non-coding RNA expression profiles in CD34⁺and in stromal cells in refractory anemia with ringed sideroblasts

Gene Locus name¹	Locus ID	ncRNA Probe Coordinates	Probe Strand	Type	Orientation relative to protein coding gene	q value²	Fold Change
Down-regulation in MDS-RARS
NEIL1	79661	chr15:73434282-73434341	+	Intronic	Sense	0.000	-4.45
BLNK	29760	chr10:97961400-97961459	-	Intronic	Sense	0.000	-3.59
KLHL5	51088	chr4:38941503-38941562	+	Intronic	Sense	0.004	-2.92
LEF1	51176	chr4:109454925-109454984	+	Intergenic	Antisense	0.001	-2.80
GABPB1	2553	chr15:48447272-48447331	+	Intergenic	Antisense	0.000	-2.55
TLE1	7088	chr9:81478431-81478490	-	Intronic	Sense	0.000	-2.30
TNFAIP3	7128	chr6:138230463-138230522	-	Intronic	Antisense	0.000	-2.21
IGSF10	285313	chr3:152637104-152637163	+	Intergenic	Sense	0.000	-2.19
CPSF6	11052	chr12:67954327-67954386	-	Intronic	Antisense	0.000	-2.16
MORN1	79906	chr1:2326963-2327014	-	Intronic	Sense	0.003	-2.15
ASAP2	8853	chr2:9299234-9299293	+	Intronic	Sense	0.003	-2.14
ST7OT1	93653	chr7:116186492-116186551	-	Intergenic	Sense	0.004	-2.13
TLE1	7088	chrX:64411696-64411755	+	Intronic	Sense	0.000	-2.12
NASP	4678	chr1:45744001-45744060	+	Intronic	Sense	0.001	-2.10
TLE1	7088	chr9:81478491-81478550	-	Intronic	Sense	0.000	-2.10
PIAS2	9063	chr18:42643244-42643303	-	Intergenic	Sense	0.000	-2.05
NUP153	9972	chr6:17815444-17815503	+	Intergenic	Sense	0.001	-2.04
ZNF76	7629	chr6:35364312-35364371	+	Intronic	Sense	0.002	-2.02
ERO1LB	56605	chr1:232705155-232705214	-	Intronic	Antisense	0.000	-1.98
CPSF6	11052	chr12:67954327-67954386	-	Intronic	Antisense	0.000	-1.97
ASXL1	171023	chr20:30410722-30410781	+	Intronic	Sense	0.001	-1.94
C5orf13	9315	chr5:111094583-111094642	+	Intronic	Antisense	0.000	-1.86
PRG4	10216	chr1:183013558-183013617	-	Intronic	Antisense	0.000	-1.86
GABPB1	2553	chr15:48448783-48448842	+	Intergenic	Antisense	0.003	-1.85
AFF1	4299	chr4:88268668-88268724	+	Intronic	Sense	0.000	-1.83
PAG1	55824	chr8:82068816-82068875	-	Intronic	Sense	0.001	-1.83
LOC441242	441242	chr7:63977853-63977912	-	Intergenic	Sense	0.003	-1.82
AASS	10157	chr7:121332812-121332871	+	Intronic	Antisense	0.001	-1.79
GCDH	2639	chr19:12871038-12871097	-	Intronic	Antisense	0.000	-1.79
SNORA71B	26776	chr20:36482692-36482751	-	Intergenic	Sense	0.001	-1.77
AFF3	3899	chr2:99698165-99698216	-	Intronic	Sense	0.004	-1.76
RBM4B	83759	chr11:66192338-66192397	+	Intronic	Sense	0.001	-1.73
Up-regulation in MDS-RARS
NR4A3	8013	chr9:99668743-99668802	+	Intronic	Sense	0.001	5.52
NR4A2	4929	chr2:157011025-157011084	-	Intronic	Sense	0.002	4.49
CCDC146	57639	chr7:76467266-76467325	-	Intronic	Antisense	0.003	4.03
MARCH1.	55016	chr4:164805948-164806007	-	Intergenic	Sense	0.002	3.77
THBS1	7057	chr15:37668391-37668450	+	Intronic	Sense	0.001	2.77
FN1	2335	chr2:216086310-216086369	+	Intronic	Antisense	0.000	2.71
RALGPS1	9649	chr9:126945696-126945747	+	Intronic	Antisense	0.000	2.70
SERPINA1	5265	chr14:93919199-93919258	+	Intronic	Antisense	0.001	2.51
EHBP1L1	254102	chr11:65104384-65104443	-	Intronic	Antisense	0.001	2.38
PPIF	10105	chr10:80781110-80781169	-	Intronic	Antisense	0.003	2.36
ANK3	288	chr10:61625808-61625867	-	Intronic	Sense	0.004	2.30
PPIF	10105	chr10:80781110-80781169	+	Intronic	Sense	0.001	2.29
ZSCAN10	84891	chr16:3082319-3082378	-	Intronic	Sense	0.004	2.24
B3GNT5	84002	chr3:184455731-184455790	+	Intronic	Sense	0.001	2.21
CYBASC3	220002	chr11:60883741-60883792	-	Intronic	Sense	0.002	2.21
NR4A2	4929	chr2:157012210-157012269	+	Intronic	Antisense	0.004	2.15
IFI30	10437	chr19:18147121-18147180	-	Intronic	Antisense	0.004	2.12
DHX38	9785	chr16:70696571-70696630	+	Intronic	Sense	0.000	2.11
FAM50A	9130	chrX:153324988-153325047	+	Intronic	Antisense	0.002	2.05
SESTD1	91404	chr2:179802621-179802672	+	Intronic	Antisense	0.000	1.91
CC2D1A	54862	chr19:13891701-13891760	-	Intronic	Antisense	0.002	1.88
SNX20	124460	chr16:49264159-49264218	-	Intronic	Sense	0.000	1.88
ICA1	3382	chr7:7932382-7932433	-	Intronic	Sense	0.000	1.86
NCOA3	8202	chr20:45714557-45714616	-	Intronic	Antisense	0.003	1.86
FRAS1	80144	chr4:79383367-79383426	+	Intronic	Sense	0.004	1.85
TMBIM6	7009	chr12:48437217-48437268	+	Intronic	Sense	0.001	1.85
CD44	960	chr11:35184235-35184294	-	Intronic	Antisense	0.000	1.83
PPP1R15A	23645	chr19:54068439-54068498	-	Intronic	Antisense	0.002	1.82
PKM2	5315	chr15:70288031-70288090	+	Intronic	Antisense	0.000	1.81
RP5-1022P6.2	56261	chr20:5491968-5492027	-	Intronic	Sense	0.002	1.81
DAGLBETA	221955	chr7:6274325-6274384	+	Intronic	Antisense	0.003	1.78
RAD51L1	5890	chr14:67951712-67951763	-	Intronic	Antisense	0.001	1.77
S100A4	6275	chr1:150330268-150330327	+	Intronic	Antisense	0.001	1.71

¹Gene locus name for intronic ncRNA is that of the protein-coding gene of the same locus; intergenic ncRNA is annotated with the name of the nearest protein-coding gene in that chromosome.
² Minimum significance among all patient Leave-one-out analyses

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ISSN: 1755-8794

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