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Table 4 Constitutively active ALK1 regulated gene expression in HMEC-1 cells after 24 hours. Gene expression profiling by Affymetrix GeneChip™ and qRT-PCR analysis for HMEC-1 cells (human microvascular endothelial cell line) infected with empty adenovirus (AdCMV3) or AdALK1QD. Listed are genes up-regulated in at least two out of three independent experiments. Cells were infected with an MOI of ~50. Gene expression was assesed after 24 hours. Gene expression profile of AdCMV3 infected cells served as reference. GeneChip™ raw data was analysed using Affymetrix MAS 4.0 comparison analysis. Listed are the mean results. Information about gene function was taken from NCBI Entrez Gene data base if not otherwise indicated. qRT-PCR based relative gene expression was calculated using the comparative ΔΔCT method. RQ represents the relative expression level (fold change) compared to the reference sample. RQMax/Min are the relative maximum/minimum expression levels of the mean expression level RQ.

From: ALK1 signalling analysis identifies angiogenesis related genes and reveals disparity between TGF-β and constitutively active receptor induced gene expression

Gene/Gene aliases [GenBank number]     
Transcription factors Gene description GeneChip™fold change (StdDev) qRT-PCR RQ (RQMax/Min) TGF-β regulated (Ref.)
Inhibitor of DNA binding 1 (ID1) (represents [S78825]) role in cell growth, senescence, and differentiation, involved in angiogenesis 2.86 (0.71) 6.56 (9.83/4.42) [6, 70]
Inhibitor of DNA binding 1B (ID1B) [S78825] role in cell growth, senescence, and differentiation, involved in angiogenesis 14* nt -
Inhibitor of DNA binding 2 (ID2) [M97796] role in cell growth and differentiation 17.6* nt [70]
Inhibitor of DNA binding 2B (ID2B) [M96843] function unknown 8.15* nt -
Ankyrin repeat domain 1 (ANKRD1)/CARP [X83703] endothelial and smooth muscle cell expression, angiogenic activity [71] 4.46 (2.80) 4.29 (13.70/2.41) [41]
High mobility group AT-hook 2 (HMGA2) [U28749] HMG proteins are essential components of the enhancesome, may act as a transcriptional regulating factor 6* nt -
Signalling molecules     
Interleukin 8 (IL-8) [M28130] inflammatory response, angiogenic factor 18.26 (10.83) 1056.07 (1686.10/666.22) [72-74]
Endothelin (EDN1)/ET-1 [J05008] vaso constrictor, involved in angiogenesis 3.36 (0.30) 3.87 (5.16/2.97) [75]
Chemokine (C-X-C motif) ligand 1 (CXCL1)/GROα1/MGSA [X54489] immune response, tumor progression, angiogenic activity 8.2* nt [70]
Bone morphogenetic protein 6 (BMP6) [M60315] induced by proinflammatory cytokines, involved in bone and cartilage development 3.8* 4.26 (5.60/3.30) [70, 76]
Heme oxygenase-1 (HO-1) [X06985] heme catabolism, beneficial in cerebrovascular events, vasodilator 3.8* nt [77]
Jagged 1 (JAG1) [U73936] ligand for notch 1, involved in angiogenesis 3.9* nt [78]
Parathyroid hormone-like hormone (PTHLH) [M24351] involved in cell proliferation, apoptosis, cancer 2.35* nt [79, 80]
Signal transduction/regulation     
SMAD6 [U59914] inhibitor of TGF-β family member signaling 2 14.2 (9.41) 14.56 (18.63/11.63) [81]
Toll-like receptor 4 (TLR4) [U93091] LPS innate immune response 4.33 (1.19) 3.98 (5.51/2.92) -
Protein tyrosine phosphatase, receptor type, J (PTPRJ)/CD148/HPTPη [D37781] involved in cell proliferation, differentiation, cell motility 3.56 (1.58) 2.08 (3.01/1.47) -
SMAD7 [AF010193] inhibitor of TGF-β family member signaling 2 7.2* nt [81]
Ras homolog gene family, member B (RHOB) [M12174] role in endosomal trafficking [82] 3.25* nt [70]
Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) [U67156] activates c-Jun N-terminal kinase (JNK) 3.2* nt -
Endoglin (ENG)/CD105 (J05481) TGF-β1, -β3 accessory receptor and signaling modulator nd 2.36 (3.08/1.84) [83]
Extracellular matrix     
Collagen 5α1 (COL5A1) [D90279] controls the initiation of collagen fibril assembly [62] 7.13 (4.27) 2.28 (2.93/1.81) [59, 60]
Serine (or cysteine) proteinase inhibitor 1 (SERPINH1)/HSP47 [D83174] assists maturation of the ECM protein type I collagen 2* nt [58]
Stress response     
DNA-damage-inducible transcript 3 (DDIT3)/ GADD153 [S40706] transcription factor, associated with cell stress and apoptosis 19.5 (2.60) 4.55 (6.42/3.27) -
DnaJ (Hsp40) homolog, subfamily B, member 1 (DNAJB1) D85429] linked to the 26S proteasome, up-regulated in bipolar disorder 3.03 (1.00) nt -
Homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 (HERPUD1) [D14695] linked to the 26S proteasome, up-regulated by Wnt-1 4.1* nt -
Cell adhesion and cytoskelet     
Neural precursor cell expressed, developmentally down-regulated 9 (NEDD9)/ HEF1 [L43821] actin filament bundle formation, cell adhesion, cytoskeleton organization and biogenesis, integrin mediated signalling pathway, regulation of cell cycle, regulation of cell growth, signal transduction 5.8 (0.95) 3.93 (5.74/2.73) [84]
Crystallin, alpha B (CRYAB) [S45630] member of the small heat shock protein (HSP20) family, assists assembly of desmin filaments [85] 11.1* nt [85, 86]
Tropomyosin 1 (alpha) (TPM1), splice variant 2 associated with the actin filaments 2.3* nt [87, 88]
Poliovirus receptor (PVR)/CD155 [M24407] also involved in the regulation of cell adhesion and cell motility [89] 2.35* nt -
Solute carrier family 3, member 2 (SLC3A2)/CD98 [M21904] activator of dibasic and neutral amino acid transport, mediates integrin signaling [90] 2.5* nt -
Miscellanous     
Leukocyte receptor cluster (LRC) member 4 (LENG4) [S82470] Over-expressed in bladder and breast carcinoma 2.1* nt -
Karyopherin alpha 3 (KPNA3) [Y12394] nuclear transport protein 91a 2.75* nt -
Ankyrin repeat domain 15 (ANKRD15) [D79994] plays a role in cell growth 2.3* nt -
Squalene epoxidase (SQLE) [D78129)] catalyzes the first oxygenation step in sterol biosynthesis 2.45* nt -
  1. The measurements of fold-change with a ~symbol in front of them are an approximation because the average difference in the reference samples were not above background; *mean of two experiments; nd, not detected; nt, not tested.