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Mech Dev 1998 Oct 01;772:95-141.
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Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning.

Gawantka V , Pollet N , Delius H , Vingron M , Pfister R , Nitsch R , Blumenstock C , Niehrs C .

In a large-scale gene expression screen 1765 randomly picked cDNAs were analyzed by whole-mount in situ hybridization in Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 204 of which are novel in Xenopus. Partial DNA sequences and expression patterns were documented and assembled into a database, 'AXelDB'. Approximately 30% of cDNAs analyzed represent differentially expressed genes and about 5% show highly regionalized expression. Novel marker genes and potential developmental regulators were found. Differential expression of mitochondrial genes was observed. Marker genes were used to study regionalization of the entire gastrula as well as the tail forming region and the epidermis of the tailbud embryo. Four 'synexpression' groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation were identified. According to their probable functional significance these groups are designated as Delta1, Bmp4, ER-import and Chromatin group. Within synexpression groups, a likely function of genes without sequence similarity can be predicted. The results indicate that synexpression groups have strong prognostic value. A cluster analysis was made by comparing gene expression patterns to derive a novel parameter, 'tissue relatedness'. In conclusion, this study describes a semi-functional approach to investigate genes expressed during early development and provides global insight into embryonic patterning.

PubMed ID: 9831640
Article link: Mech Dev

Species referenced: Xenopus
Genes referenced: 10a1.1 actl6a adam13 ag1 aifm2 akirin1 aldoa anxa5 apobec2 arl6ip1 arpc1b asl atp5mc3 atp6ap2 atp6v0c bambi blvra bmp4 bsg btg1 canx cbx3 ccdc50 ccnb1.2 ccnb3 cd63 cd81 cd9 cdk1 cdk4 cdknx churc1 cirbp cited4 ckap4 ckb cldn6.1 clic4 cluap1 copz1 cox5a cox7c crx ctnnbl1 cybrd1 cycs cyld cyp26a1 cystm1 ddit4 derl2 dhcr7 dhx32 dkc1 dkk1 dll1 eef1a1 eef1a1o eef2.1 efnb2 eif1 eif3b eif4g2 epha4 f11r fbxw4 fech fgfr4 ficd fn1 foxa4 frzb fth1.1 g0s2 gale gby gfpt1 gfpt2 glud1 gnb1 gpr4l.2 gs17 h1-6 h2az1 h3-5 hal.1 hao1 has1 hes5.5 hes5.6 hes5.7 hes6.1 hes7.2 hesx1 higd1a hmgb2 hmgb3 hmgn1 hmgn2 hmgn3 hnrnpa1 hnrnpa2b1 hnrnpab hnrnpdl hnrnpk hnrnpu hoxd1 hsp90b1 id2 id3 ilf2 ipo7 isyna1 itln1 jpt1 kcnk6 klf6 klhdc4 krt12.4 krt12.5 krt18.1 krt7 krt70 krt8.1 lbh ldhb lmo7 lsp1 magoh marcks marcksl1 MGC75753 mst1 msx2 mthfd2 myf5 myl1 naca nap1l1 nop56 nop58 not nradd nrarp nucks1 nudt9 odad2 odc1 ogt otx2 p4hb pax3 pcdh8.2 pcna perp pfkfb1 pitx2 plekhg4 plekho1 plod2 pnhd pnrc2 post pou5f3 ppdpf prdm1 preb prelid1 prmt1 psma2 ptma ptmap12 rbm28 rbm5 rcc1 rcl1 rcn3 rcor2 rhebl1 rhou rilpl1 rpa1 rpl29 rpl30 rpl37a rps2 rps20 rps3a scamp2 sec61a1 sec61b sec61g sema3a sesn2 sfpq slc22a4 slc25a20 slc25a20l slc25a24 slc30a2 sltm snu13 sox15 sox17a sox2 sox3 sp5l spint2 srsf2 srsf3 ss18 ssr2 ssr3 stard10 stmn1 tagln2 tardbp tbpl1 tbxt tmem126a tmpo tmsb4x tpt1 tuba1cl.3 tuba4b tuba5 tubb4a uap1 upk2 upk3a vdac2 ventx1.2 ventx2 XB22041735 XB5863530 XB5967085 xmc ywhaq znf326 znf451 znf608

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