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PostPosted: Thu Sep 24, 2015 6:39 am 
Hi,

I've been successfully doing some (human) analysis with GREAT 3.0. After completion of the analysis, I downloaded all the region-gene associations. I also downloaded the file with the complete set of human genes (and their corresponding TSS) that are used in GREAT 2.0 (found on the page http://bejerano.stanford.edu/help/display/GREAT/Genes). However, I've noticed that out of the 1684 genes associated with a region based on GREAT results, there are 122 genes that are not found on the complete gene file. Is that because the gene list file available for download is out of date? To better illustrate the case, down below I pasted the list of missing genes.

I would be helpful if you could help me figure this out. Thanks a lot!!

AGO1
AGO4
AIFM3
AMER1
ANKRD39
ANKRD52
ASIC1
ATRAID
AUNIP
BCL2L2
BLOC1S5-TXNDC5
BOD1L1
C10orf95
C18orf25
C1orf174
C22orf29
CACTIN
CATSPERD
CCDC12
CCDC180
CCDC87
CEP170B
CHCHD5
CHKB-CPT1B
COBLL1
CTSL
DENND4B
DESI1
DPCD
ECH1
EFCC1
ELP5
EMC6
ENSG00000105520
ENSG00000249240
ENSG00000251537
ENSG00000255292
ENSG00000256566
ENSG00000258728
ENSG00000259529
ENSG00000259784
ENSG00000262302
ENSG00000262660
ENSG00000263620
ENSG00000265264
ENSG00000265818
ENSG00000267001
ENSG00000267157
ENSG00000268107
ENSG00000268133
ENSG00000268173
ENSG00000268750
ENSG00000269533
ENSG00000269545
ENSG00000269590
ENSG00000271698
ENSG00000272333
ENTHD2
EVA1C
FAM76B
FAM89B
FBRS
FBXL22
GALNT18
GOPC
HID1
HSD17B8
HYPK
IL10RB
KDM8
KLHL42
KMT2A
LAMTOR5
MRPL12
MSANTD3
MTFP1
NADK2
NAT6
NBAS
NDUFA13
NELFB
NOP9
NRROS
NTMT1
OXLD1
PABPN1
PCDHGA10
PCDHGB7
PET100
PHLDB3
PHYKPL
PLEKHO2
PPP1R27
PPP1R3E
PPP2CA
PPP5D1
PRAF2
PRDM11
PTGES3L-AARSD1
PYURF
RPP25L
SAMD4B
SLC25A51
SLC25A53
SLC52A2
SLX4IP
SMIM20
SMIM3
SMIM4
STMND1
TANGO2
TEX38
TIMM10B
TMEM110
TMEM249
TMEM253
TRAPPC2P1
TRIM6
TRMT10B
TWF2
VPS9D1
WDR81
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 Post subject: GREAT 3.0 Gene set
PostPosted: Wed Sep 30, 2015 8:38 am 
Site Admin
Hello,

We have updated the GREAT documentation, and you can now find the set of genes that GREAT 3.0 uses (and the corresponding Ensembl ID) here: http://bejerano.stanford.edu/help/display/GREAT/Genes

Best,
The GREAT Team
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