I want to compare primary HUVECs with my immortalized HUVECs. I have done microarrays and was wondering if I can somewhere (some database etc) find a list of cell type specific genes (which, in my case, would be endothelial cell specific genes). Any kind of help would be appreciated.
Dear Thomas, thanks for your response. I have already done several advanced functional testings for my cells, both in vitro as well as in vivo and the data looks pretty good. In addition, I would definitely do the whole transcriptome analysis but was wondering if I can exclusively look at the genes specific to endothelial cells, esp. HUVECs and if such a list is available in some kind of database. There is at least on such paper that compares endothelial cell specific genes (Ho et al. 2003 Physiol Genomics 13: 249-262).
Hi Muhammad!
There is an article from Patrick Brown's lab from 2003:
Chi JT1, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO.
Endothelial cell diversity revealed by global expression profiling.
Proc Natl Acad Sci U S A. 2003 Sep 16;100(19):10623-8.
Then you may take a closer look at Gene Omnibus microarray dataset GSE3239. There they have identified genes more abundant in endothelial cells (EC), but low in smooth muscle cells (SMC), fibroblasts and epithelial cells. The list below represents fold differences between mRNA expression levels in EC and SMC:
Gene ArterialEC VenousEC
SOX17 1,21 16,87
MYRIP 1,63 10,54
SRGN 1,72 1,81
LIPG 1,95 9,65
ALDH1A1 1,97 19,29
IGF2BP3 2,29 5,76
SEC14L1 2,57 4,49
TEK 2,83 8,61
PROCR 2,92 1,96
ITM2A 2,95 23,07
ESM1 3,43 2,11
ARHGDIB 3,77 5,00
HOXB7 4,71 3,73
PTPRB 5,36 9,58
THBS1 5,48 5,47
MYCT1 5,87 9,37
HECW2 6,44 9,76
RASIP1 7,67 9,72
CALCRL 8,31 35,38
PGF 8,46 4,14
PCDH1 8,50 19,51
BST2 8,81 0,81
TINAGL1 9,26 6,39
NRN1 10,02 14,73
CGNL1 10,24 17,49
IFI27 10,44 3,30
HCLS1 11,14 10,54
ANGPT2 12,14 10,91
EDN1 12,15 19,46
GIMAP7 12,17 23,84
IL1RL1 12,61 18,68
MMRN1 13,13 152,78
C17orf72 13,31 7,66
IFI27 13,93 3,57
MLZE 14,37 20,91
RAPGEF5 14,40 31,24
AL576606 14,50 1,31
EMCN 14,88 18,24
FRMD4B 15,06 18,14
MMRN1 15,38 150,30
GATA3 15,66 2,35
ABI3 16,02 19,85
PTPRE 16,35 33,37
LYL1 16,82 29,30
FGD5 16,97 34,99
EGFL7 18,16 67,55
ESAM 18,65 20,07
ASRGL1 19,40 38,06
SHE 19,44 35,15
RNASE1 19,53 94,28
CLDN5 20,28 48,54
BI823044 20,45 152,97
CDH5 20,84 183,71
CLEC1A 21,14 60,02
GIMAP6 22,08 119,60
MPZL2 22,84 219,25
PRKAR2B 23,02 42,90
TIE1 23,26 77,59
ERG 23,90 61,29
LAPTM5 24,13 58,32
FBP1 24,32 28,03
TM4SF18 25,84 53,04
BQ717190 26,35 37,22
MGAT4A 28,26 143,79
GIMAP4 28,97 225,52
AA480009 29,10 61,80
ICAM2 29,60 61,18
FAM124B 30,65 27,04
NMNAT1 31,47 50,28
CYTL1 31,51 175,05
BMX 32,43 229,34
C10orf58 44,67 80,90
FAM107A 49,62 225,09
CXorf36 67,49 85,36
Hi Muhammad,
CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/ or http://bio-bigdata.hrbmu.edu.cn/CellMarker/) is a database of cell markers based on tissue and cell type.
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