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Table 3 Top 50 brain-specific and bottom ten brain underexpressed genes (in italics) identified by integrated PEM scores from Gene Expression Atlas, SAGEmap and TissueInfo.

From: Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases

%PEM a UniGene cluster LocusLink symbol Description and references
76% Hs.6535 n/a novel cDNA clone, FLJ33742 fis, highly similar to Homo sapiens BNPI mRNA for brain-specific Na-dependent inorganic phosphate cotransporter (GenBank AK091061)
76% Hs.143535 CAMK2A calcium/calmodulin-dependent protein kinase, implied in control of fear and aggression [18]
75% Hs.78854 ATP1B2 ATPase, Na+/K+ transporting [19, 20]
74% Hs.194301 MAP1A microtubule-associated protein, expressed strongly in brain, spinal cord and weakly in muscle [21]
73% Hs.84389 SNAP25 synaptosomal associated protein; one of SNARE proteins required for neuronal exocytosis [22]
72% Hs.2288 VSNL1 visinin like 1; known to be expressed in neuronal cells in retina [23]
72% Hs.1787 PLP1 lipophilin – the primary constituent of myelin [24]
72% Hs.296184 GNAO1 G protein alpha activating activity polypeptide O; multiple neurological abnormalities in knock-out mice [25]; cloned from brain [26]
71% Hs.75819 GPM6A neuronal membrane glycoprotein M6A; similar to myelin proteolipid protein [27]
71% Hs.69547 MBP myelin basic protein [28]
70% Hs.74565 APLP1 amyloid beta (A4) precursor-like protein 1 [29]
69% Hs.6139 SYNGR1 synaptogyrin 1 [30]
69% Hs.154679 SYT1 synaptotagmin 1 [31]
68% Hs.20912 APCL brain-specific adenomatous polyposis coli (APC) homologue [32]
66% Hs.5422 GPM6B neuronal membrane glycoprotein M6B, highly similar to the myelin proteolipid protein [27]
66% Hs.79000 GAP43 neuromodulin, implied in axon guidance [33]
65% Hs.22777 CA11 carbonic anhydrase XI; brain-specific carbonic anhydrase isosyme [34]
65% Hs.239356 STXB1 syntaxin binding protein 1 [35]
65% Hs.182859 LFG lifeguard (alias neuromembrane protein 35) [36]
65% Hs.7979 SV2 synaptic vesicle glycoprotein 2 [37]
64% Hs.322430 NDRG4 ndrg family member 4, expressed in brain and heart [38]
64% Hs.74554 SYT11 synaptotagmin 11; identified by genomic screen with highly conserved synaptotagmin motif [39]
64% Hs.82749 TM4SF2 transmembrane 4 superfamily member 2; contains a trinucleotide repeat [40], implied in X linked mental retardation [41], implied in axon guidance
64% Hs.169401 APOE apolipoprotein E; implied in Alzheimer's disease [42]
63% Hs.166161 DNM1 dynamin 1 – brain expression at least 30-fold higher than in other tissues [43]
62% Hs.6164 NECL1 nectin-like protein 1; alias brain immunoglobulin receptor precursor (unpublished, GenBank NM_021189)
62% Hs.76888 INA internexin – neuronal intermediate filament protein alpha [44]
61% Hs.146580 ENO2 enolase 2 – neuronal-specific enolase [45]
61% Hs.90005 STMN2 stathmin-like 2; expressed in neuronal growth cones [46]
61% Hs.226133 GAS7 growth arrest-specific 7; expressed in neurons and growth-arrested fibroblasts [47]
60% Hs.155524 PNUTL2 septin 4; human orthologue of the mouse h5 brain protein [48]; involved in cell-division control; expressed in brain and, an alternatively spliced form, in heart [49]
60% Hs.117546 NNAT neuronatin; known to contain a 5' neurospecific silencer element which controls brain-specific expression [50]; possible role in brain development
60% Hs.155247 ALDOC brain-type aldolase; fructose-bisphosphate aldolase C [51]
60% Hs.7357 CLIPR-59 microtubule-binding protein involved in Golgi targeting; known to be preferentially expressed in brain [52]
60% Hs.74583 SPOCK2 sparc/osteonectin like; testican 2; calcium-binding proteoglycan specific to brain; expressed in many neuronal cell types in olfactory bulb, cerebral cortex, thalamus, hippocampus, cerebellum, and medulla [53]
60% Hs.80395 MAL hydrophobic integral membrane lipoprotein; a component of myelin [54]
60% Hs.6349 BC008967 novel protein BC008967
60% Hs.6755 RPIP8 RaP2 interacting protein; belongs to Ras family; expressed principally in brain [55]
60% Hs.75090 SPRING involved in synaptic exocytosis; expressed only in brain [56]
60% Hs.90063 NCALD neurocalcin delta; calcium-binding protein; expressed preferentially in brain [57]
58% Hs.83384 S100B calcium-binding protein S100; expressed in glia, astrocytes and neurons [58]
58% Hs.104925 ENC1 ectodermal-neural cortex; p53 induced gene; expressed preferentially in brain, particularly in amygdala and hippocampus [59]
58% Hs.7782 PNMA2 onconeuronal antigen MA2; expressed in brain and testis [60]
58% Hs.8526 B3GNT6 beta-1,3-N-acetylglucosaminyltransferase 6; expressed preferentially in foetal and adult brain [61]
56% Hs.125359 THY1 Thy-1 cell surface antigen; expressed in brain and on some T cells; neuronal expression pattern changes in development suggesting role in neurogenesis [62]
56% Hs.194534 VAMP2 synaptobrevin 2; one of proteins involved in fusion of synaptic vesicles with the presynaptic membrane [63]
56% Hs.31463 ELMO1 engulfment and cell motility 1; orthologue of C. elegans gene ced-12; has two isforms – 4.4 kb expressed ubiquitously and 2.4 kb expressed only in brain [64]
55% Hs.3763 APBB1 amyloid beta (A4) precursor protein-binding; expressed preferentially in brain [65]
55% Hs.286055 CHN2 chimerin 2; expressed preferentially in cerebellum in granule cells [66]
55% Hs.12305 DKFZP566B183 novel protein DKFZP566B183
-50% Hs.80988 COL6A3 collagen type VI alpha 3 chain; type 3 alpha chain of a beaded filament collagen found in most connective tissues[67]
-50% Hs.79914 LUM lumican, a keratan sulfate proteoglycan known to be abundant in the corneal stroma and collagenous matrices of the heart, skeletal muscle, aorta, and intervertebral discs[68]
-51% Hs.38972 TSPAN-1 tetraspan 1[69]
-53% Hs.692 EPCAM epithelial cellular adhesion molecule; expressed only on epithelial cells[70]
-56% Hs.297681 SERPINA1 antitrypsin, primarily expressed in liver[71]
-57% Hs.5372 CLDN4 claudin 4; expressed in kidney, small intestine, lung, heart, liver, and skeletal muscle; no expression was found in brain or spleen[72]
-57% Hs.81892 KIAA0101 identified in the Kazusa large-scale cDNA sequencing project [73]; northern blot revealed expression in many tissues but signal is completely absent from brain
-58% Hs.195850 KRT5 keratin 5; expressed in many epithelia including mammary epithelial cells and squamous epithelia lining the upper digestive tract[74]
-59% Hs.65114 KRT18 keratin 18 [75]; expressed in many epithelia
-60% Hs.182265 KRT19 keratin 19; found predominantly in the periderm – the transient layer that surrounds the developing epidermis[76]
  1. a Integrated PEM score, calculated as the average of PEMGEA/PEMGEAmax, PEMSAGEMAP/PEMSAGEMAPmax, PEMTISSUEINFO/PEMTISSUEINFOmax, where "max" refers to the maximum PEM value encountered in the tissue. This weighting scheme was used because brain microarray PEM values were several fold higher than those for SAGE and EST (PEMGEAmax = 5.21, PEMSAGEMAPmax = 1.19, PEMTISSUEINFOmax = 1.15)