Selected list of up- and downregulated genes
| Gene symbol . | Probe set ID . | Mutant/wild type . | Mutant/heterozygote . | GOID . | Functional annotation . |
|---|---|---|---|---|---|
| Sox2* | 100009_r_at | 1.3 | 1.3 | (GOID:6350) Transcription | |
| Pem | 101368_at | 0.7 | 0.9 | (GOID:6350) Transcription | |
| Dab2 | 98045_s_at | 0.6 | 0.7 | (GOID:9653) Morphogenesis | |
| Gbx2* | 94200_at | —5.4 | —4.4 | (GOID:6350) Transcription | Pat |
| Hoxa1 | 95297_at | —5.1 | —4.5 | (GOID:7389) Pattern Specification | Pat |
| Cdx1 | 103477_at | —4.2 | —4.9 | (GOID:6350) Transcription | Pat |
| Raldh2 | 101707_at | —3.6 | —3.4 | (GOID:1523) Retinoid metabolism | Pat |
| twist | 98028_at | —3.2 | —3.6 | (GOID:6350) Transcription | Pat |
| Hoxb1* | 93888_at | —1.7 | —1.8 | (GOID:7389) Pattern Specification | Pat |
| Wnt5a | 99390_at | —1.6 | —1.8 | (GOID:9653) Morphogenesis | Pat |
| Hoxb2 | 106927_at | —1.5 | —1.4 | (GOID:7389) Pattern Specification | Pat |
| Wnt3a* | 102667_at | —2.9 | —3.2 | (GOID:9653) Morphogenesis | Pat, Mes |
| Tbx6 | 93611_at | —1.6 | —1.8 | (GOID:6350) Transcription | Pat, Mes |
| T | 93941_at | —1.4 | —1.4 | (GOID:6350) Transcription | Pat, Mes |
| Meox1 | 98419_at | —1 | —0.7 | (GOID:6350) Transcription | Pat, Mes |
| FGFR1 | 97509_f_at | —0.6 | —0.6 | (GOID:7154) Cell Communication | Pat, Mes |
| Follistatin | 98817_at | —0.6 | —1 | TGF-beta signaling pathway | Pat, Mes |
| Lef1 | 103628_at | —0.5 | —0.6 | (GOID:6350) Transcription | Pat, Mes |
| Axin2* | 163891_at | —0.4 | 0.1 | (GOID:7154) Cell Communication | Pat, Mes |
| Dll1* | 92931_at | —2 | —1.5 | (GOID:7389) Pattern Specification | Pat, Mes, L-R |
| Notch1* | 97497_at | —1.3 | —0.8 | (GOID:7389) Pattern Specification | Pat, Mes, L-R |
| Foxj1 | 98831_at | —1.2 | —1 | (GOID:6350) Transcription | L-R |
| Sox17 | 92996_at | —0.8 | —0.7 | (GOID:6350) Transcription | En |
| EST6† | 114959_at | —5 | —4.8 | RIKEN cDNA C030045D06 gene | |
| EST16† | 138065_at | —4.9 | —3.7 | None available | |
| Wnt8* | 99361_at | —2.4 | —3 | (GOID:7154) Cell Communication | |
| Fragilis2† | 160254_at | —1.6 | —1.7 | Family of IFN-inducible genes | |
| EST10† | 97386_at | —1.5 | —1.6 | Similar to integrase of retrovirus | |
| Crabp1 | 98108_at | —1.5 | —1.3 | (GOID:5501) Retinoid binding | |
| Smarcd3 | 108488_at | —1.4 | —1.5 | SWI/SNF related regulator of chromatin | |
| NFkB | 98427_s_at | —1.3 | —1.1 | (GOID:6350) Transcription | |
| Frzb1* | 104672_at | —1.1 | —1 | (GOID:7275) Development | |
| Scap2† | 102012_at | —1 | —0.5 | Src associated phosphoprotein 2 | |
| Rbp1 | 104716_at | —1 | —1 | (GOID:1523) Retinoid metabolism | |
| Punc† | 94117_f_at | —1 | —1 | (GOID:7154) Cell Communication | |
| Irx3 | 99034_at | —1 | —0.9 | (GOID:6350) Transcription | |
| AI447312 | 106222_at | —0.8 | —1 | Hypothetical aminotransferases class-II | |
| Grsf1† | 96684_at | —0.8 | —0.7 | G-rich RNA sequence binding factor 1 | |
| Zic3† | 98330_at | —0.8 | —0.7 | (GOID:6350) Transcription |
| Gene symbol . | Probe set ID . | Mutant/wild type . | Mutant/heterozygote . | GOID . | Functional annotation . |
|---|---|---|---|---|---|
| Sox2* | 100009_r_at | 1.3 | 1.3 | (GOID:6350) Transcription | |
| Pem | 101368_at | 0.7 | 0.9 | (GOID:6350) Transcription | |
| Dab2 | 98045_s_at | 0.6 | 0.7 | (GOID:9653) Morphogenesis | |
| Gbx2* | 94200_at | —5.4 | —4.4 | (GOID:6350) Transcription | Pat |
| Hoxa1 | 95297_at | —5.1 | —4.5 | (GOID:7389) Pattern Specification | Pat |
| Cdx1 | 103477_at | —4.2 | —4.9 | (GOID:6350) Transcription | Pat |
| Raldh2 | 101707_at | —3.6 | —3.4 | (GOID:1523) Retinoid metabolism | Pat |
| twist | 98028_at | —3.2 | —3.6 | (GOID:6350) Transcription | Pat |
| Hoxb1* | 93888_at | —1.7 | —1.8 | (GOID:7389) Pattern Specification | Pat |
| Wnt5a | 99390_at | —1.6 | —1.8 | (GOID:9653) Morphogenesis | Pat |
| Hoxb2 | 106927_at | —1.5 | —1.4 | (GOID:7389) Pattern Specification | Pat |
| Wnt3a* | 102667_at | —2.9 | —3.2 | (GOID:9653) Morphogenesis | Pat, Mes |
| Tbx6 | 93611_at | —1.6 | —1.8 | (GOID:6350) Transcription | Pat, Mes |
| T | 93941_at | —1.4 | —1.4 | (GOID:6350) Transcription | Pat, Mes |
| Meox1 | 98419_at | —1 | —0.7 | (GOID:6350) Transcription | Pat, Mes |
| FGFR1 | 97509_f_at | —0.6 | —0.6 | (GOID:7154) Cell Communication | Pat, Mes |
| Follistatin | 98817_at | —0.6 | —1 | TGF-beta signaling pathway | Pat, Mes |
| Lef1 | 103628_at | —0.5 | —0.6 | (GOID:6350) Transcription | Pat, Mes |
| Axin2* | 163891_at | —0.4 | 0.1 | (GOID:7154) Cell Communication | Pat, Mes |
| Dll1* | 92931_at | —2 | —1.5 | (GOID:7389) Pattern Specification | Pat, Mes, L-R |
| Notch1* | 97497_at | —1.3 | —0.8 | (GOID:7389) Pattern Specification | Pat, Mes, L-R |
| Foxj1 | 98831_at | —1.2 | —1 | (GOID:6350) Transcription | L-R |
| Sox17 | 92996_at | —0.8 | —0.7 | (GOID:6350) Transcription | En |
| EST6† | 114959_at | —5 | —4.8 | RIKEN cDNA C030045D06 gene | |
| EST16† | 138065_at | —4.9 | —3.7 | None available | |
| Wnt8* | 99361_at | —2.4 | —3 | (GOID:7154) Cell Communication | |
| Fragilis2† | 160254_at | —1.6 | —1.7 | Family of IFN-inducible genes | |
| EST10† | 97386_at | —1.5 | —1.6 | Similar to integrase of retrovirus | |
| Crabp1 | 98108_at | —1.5 | —1.3 | (GOID:5501) Retinoid binding | |
| Smarcd3 | 108488_at | —1.4 | —1.5 | SWI/SNF related regulator of chromatin | |
| NFkB | 98427_s_at | —1.3 | —1.1 | (GOID:6350) Transcription | |
| Frzb1* | 104672_at | —1.1 | —1 | (GOID:7275) Development | |
| Scap2† | 102012_at | —1 | —0.5 | Src associated phosphoprotein 2 | |
| Rbp1 | 104716_at | —1 | —1 | (GOID:1523) Retinoid metabolism | |
| Punc† | 94117_f_at | —1 | —1 | (GOID:7154) Cell Communication | |
| Irx3 | 99034_at | —1 | —0.9 | (GOID:6350) Transcription | |
| AI447312 | 106222_at | —0.8 | —1 | Hypothetical aminotransferases class-II | |
| Grsf1† | 96684_at | —0.8 | —0.7 | G-rich RNA sequence binding factor 1 | |
| Zic3† | 98330_at | —0.8 | —0.7 | (GOID:6350) Transcription |
Genes were annotated using the Affymetrix Netaffx and NCBI databases.
The Gene symbol, Affymetrix probeset ID, signal log2 ratio for both comparisons, a GO-term ID (GOID) and a functional annotation are given.
Pat, patterning and morphogenesis; Mes, paraxial mesoderm and somites; En,endoderm formation; L-R, left-right axis determination.
Genes whose differential expression was confirmed by in situ hybridization
Genes for which the expression pattern was tested in wild-type embryos