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.
%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 | |
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 http://www.kazusa.or.jp/huge/gfpage/KIAA0101/ |
-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] |