Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

C. Long ncRNAs Appendix
Table C.1: Differentially expressed non-coding RNAs.
Tag Accession Description In gene desert? PubMedID(s) Differential expression results Normalised tag counts
log 2(F C) p-value FDR G144ED G144 G166 G179 CB541 CB660
HOTAIRM1, a ncRNA from the
HOXA locus. There is evidence
CCGCCTTAATAAATGTA BC031342
No 19144990 Inf 7.9E-10 4.3E-06 174.7 158.7 129.8 206.3 0.0 0.0
that it might regulate HOXA gene
expression.
NEAT1, a ncRNA involved in
TACATAATTACTAATCA NR_028272 paraspeckle formation and regu- Yes 20137068; 21170033 4.32 1.6E-06 2.2E-03 123.4 627.4 775.4 1927.1 18.5 91.8
lated during NS cell differentiation.
CDKN2BAS, an antisense transcript
to CDKN2B that appears
TGGATAAACAAAATGAA NR_003529 to function in Polycomb-mediated No 18185590; 20541999 Inf 1.4E-05 1.3E-02 18.0 33.6 125.8 0.0 0.0 0.0
repression of tumor suppressors
CDKN2A and CDKN2B.
Transcript from the opposite strand
TATCCCCAAATAAACAA NR_015382
No None 4.42 3.2E-05 2.4E-02 151.4 123.2 332.4 135.3 9.3 9.4
of CD27.
Transcript from the opposite strand
ATGGCACCATATTGTGT NR_015377
No None -7.08 2.5E-05 2.0E-02 0.0 0.0 2.2 0.0 136.9 58.3
of PAX8.
Transcript from the opposite strand
CCTGACCCTGCATCCCT BC013229
No None Inf 1.4E-04 7.5E-02 1.7 0.0 36.9 68.3 0.0 0.0
of MCF2L2.
Transcript from the opposite strand
TAGAACGGTGTTCCTCC BM977209
No None Inf 1.7E-05 1.5E-02 0.0 0.0 121.6 24.7 0.0 0.0
of TXNRD1.
Transcript from CDKN2B intron
ACAAACAAAAGCCTTCC DB099927
No None Inf 1.4E-05 1.3E-02 41.9 105.5 51.8 0.0 0.0 0.0
(sense strand).
Transcript from gene desert near
ATTACATTTATGTCCTT BC015429 DKK1. Correlated with DKK1 ex- Yes None Inf 2.8E-09 1.1E-05 0.0 0.0 389.5 18.0 0.0 0.0
pression.
TAACTGATCCTTAGATA BQ957425 Transcript from gene desert. Yes None Inf 2.0E-04 9.9E-02 0.0 0.0 66.8 30.8 0.0 0.0
GAAACATTCCAAACCTA AK094154 Transcript from gene desert. Yes None Inf 1.3E-10 9.9E-07 0.0 0.0 328.5 243.9 0.0 0.0
CAAATAAACTTTATACC BC063641 Transcript downstream of PRRG4. No None 7.53 2.4E-11 2.3E-07 4.2 68.0 267.3 1381.8 0.0 5.9
Transcript between CTSC and
GCTTTATTTTTTCTGCT BC038205 GRM5. Correlated with CTSC Yes None 7.46 5.4E-07 8.7E-04 54.0 96.2 49.6 126.3 0.0 1.0
expression.
GAGCCCAGACTAGATGG BF031226 Transcript from gene desert. Yes None Inf 3.9E-05 2.8E-02 1.4 0.0 30.7 99.7 0.0 0.0
274
Yes 12082533; 15872005 -Inf 3.5E-07 6.3E-04 0.0 0.0 0.0 0.0 21.8 283.9
The tag is in last intron of
ncRNA NCRMS, perhaps detecting
an NCRMS isoform. NCRMS might
be a host transcript for mir-1251
and mir-135a-2. The tag also coincides
with a SINE repeat.
AAATATTAGTTTTTCTT CX868766