Table 2.

Ciona intestinalis genes, identified by microarray analysis,that have an altered level of expression at 25 hpf when treated with U0126 MEK inhibitor

Genes upregulated by U0126 treatment
Chip featureKyotoGrail gene modelJGI version 1 gene modelIdentity and/or GO functionClassReferences*In situ
26102 2004.972.4.1 ci0100137018 IPI:IPI00114285. 1| NP_034492|ENSEMBL: Glutathione transferase omega 1 (Woods et al., 2004)  
0421 2005.972.4.1    (Davidson and Swalla, 2002)  
12481 2004.573.7.1 ci010046721 Q21945 Hypothetical 23.3 kDa protein Caenorhabditis elegans; KOG1695 Glutathione-S-transferase DI (Woods et al., 2004)  
1849 2005.573.7.1    (Davidson and Swalla, 2002)  
40275 2004.59.32.1 ci0100130315 dme:CG17986 CG17986 gene product; KOG1208 dehydrogenases with different specificities (Ci-dhg  
 2005.59.33.1      
6534 2004.158.11.1 ci0100139721 gi|3511226|gb|AAC79993.1| glutathione S-transferase [Anopheles gambiae(Woods et al., 2004)  
37997 2005.158.9.1    (Davidson and Swalla, 2002)  
34118 2004.1136.5.1 ci0100152173 gi|14041150|emb|CAC38761.1| leukotriene B4[Geodia cydonium  
 2005.1136.5.1      
16193 No model found ci0100153140 hsa:6819 SULT1C1; sulfotransferase family, cytosolic, 1C, member 1   
20200 2004.149.8.1 ci0100146267 gi|1008046|dbj|BAA09124.1| cytochrome P-450[Xenopus laevis(Woods et al., 2004)  
 2005.149.9.1      
22885 2004.350.2.1 ci0100140514 gi|21299591|gb|EAA11736.1|agCP5786 [Anopheles gambiae str. PEST]; KOG1205 Predicted dehydrogenase   
 2005.350.2.1      
10258 2004.280.16.1 ci0100145025 gi|13432102|sp|P08243|ASNS_HUMAN asparagine synthetase [glutamine-hydrolyzing] (Glutamine-dependent asparagine synthetase)   
 005.280.15.1      
36290 2005.2.118.1 ci0100144489 IPI:IPI00556036 Inter-alpha fragment; Trypsin inhibitor heavy chain 3 DII   
 2004.2.117.1      
35270 2004.12.8.1 ci0100142643 gi|21703186|gb|AAM76090.1| Vwa1 protein[Boltenia villosa] (Ci-Vwa1c(Davidson and Swalla, 2002)  
 2005.12.7.1      
20083 No model found No model found No hit found DII   
Genes upregulated by U0126 treatment
Chip featureKyotoGrail gene modelJGI version 1 gene modelIdentity and/or GO functionClassReferences*In situ
26102 2004.972.4.1 ci0100137018 IPI:IPI00114285. 1| NP_034492|ENSEMBL: Glutathione transferase omega 1 (Woods et al., 2004)  
0421 2005.972.4.1    (Davidson and Swalla, 2002)  
12481 2004.573.7.1 ci010046721 Q21945 Hypothetical 23.3 kDa protein Caenorhabditis elegans; KOG1695 Glutathione-S-transferase DI (Woods et al., 2004)  
1849 2005.573.7.1    (Davidson and Swalla, 2002)  
40275 2004.59.32.1 ci0100130315 dme:CG17986 CG17986 gene product; KOG1208 dehydrogenases with different specificities (Ci-dhg  
 2005.59.33.1      
6534 2004.158.11.1 ci0100139721 gi|3511226|gb|AAC79993.1| glutathione S-transferase [Anopheles gambiae(Woods et al., 2004)  
37997 2005.158.9.1    (Davidson and Swalla, 2002)  
34118 2004.1136.5.1 ci0100152173 gi|14041150|emb|CAC38761.1| leukotriene B4[Geodia cydonium  
 2005.1136.5.1      
16193 No model found ci0100153140 hsa:6819 SULT1C1; sulfotransferase family, cytosolic, 1C, member 1   
20200 2004.149.8.1 ci0100146267 gi|1008046|dbj|BAA09124.1| cytochrome P-450[Xenopus laevis(Woods et al., 2004)  
 2005.149.9.1      
22885 2004.350.2.1 ci0100140514 gi|21299591|gb|EAA11736.1|agCP5786 [Anopheles gambiae str. PEST]; KOG1205 Predicted dehydrogenase   
 2005.350.2.1      
10258 2004.280.16.1 ci0100145025 gi|13432102|sp|P08243|ASNS_HUMAN asparagine synthetase [glutamine-hydrolyzing] (Glutamine-dependent asparagine synthetase)   
 005.280.15.1      
36290 2005.2.118.1 ci0100144489 IPI:IPI00556036 Inter-alpha fragment; Trypsin inhibitor heavy chain 3 DII   
 2004.2.117.1      
35270 2004.12.8.1 ci0100142643 gi|21703186|gb|AAM76090.1| Vwa1 protein[Boltenia villosa] (Ci-Vwa1c(Davidson and Swalla, 2002)  
 2005.12.7.1      
20083 No model found No model found No hit found DII   
Genes downregulated by U0126 treatment
Chip featureKyotoGrail gene modelJGI version 1 gene modelIdentityClassReferences*In situ
21484 2004.18.40.1 ci0100145332 NM112885 protein binding/ubiquitin protein ligase/Zn-ion binding[Arabidopsis thalianaDI   
28505 2004.18.40.2      
 2005.18.42.1      
 2005.18.42.2      
40650 2004.132.46.1 No model found Rat nuclear pore complex N153 (Nup 153) sp:P49791   
 2005.132.44.1      
10051 2004.43.38.1 ci0100148033 O61785 (O61785) Hypothetical 29.0 kDa protein [Caenorhabditis elegansDI   
 2005.43.38.1      
19579 2004.58.13.1 ci0100131282 gi|19032245|emb|CAD24308.1| putative coagulation serine protease [Ciona intestinalis(Davidson and Swalla, 2002)  
 2005.58.13.1      
20246 2004.305.11.1 ci0100149359 IPI:IPI00001729 Matrix metalloprotease-24-precursor (Ci-Mx  
30477 2005.305.12.1      
14883 2004.82.31.1 ci0100147945 IPI:IPI00112858.1|NP_073725| Polydom protein precursor [Homo sapiens] (Ci-polydom  
 2005.82.27.1      
 2005.82.27.2      
 2005.82.27.3      
41165 2004.18.53.1 ci0100146122 gi|4468715|emb|CAB38105.1| beta-microseminoprotein[Saguinus oedipusDI   
 2005.18.55.1      
33659 2004.163.38.1 ci0100139661 gi|12381859|dbj|BAB21104.2| SMaf1 [Danio rerio]. 0006355, regulation of transcription, DNA-dependent   
25306 2005.163.33.1      
6228       
23758 2004.272.9.1 ci0100141699 No hit found DII   
2153 2005.272.10.1      
10333 2004.51.20.1 ci0100154804 IPI:IPI00165235.1| Similar to carboxypeptidase Z [Homo sapiens] (Ci-carboxypeptidase(Nakayama et al., 2001)(Nakayama et al., 2002)  
39015 2005.51.23.1      
20529       
41121       
29978 2005.96.7.1 ci0100141212 gi|17538868|ref|NP_502249.1|ankyrin repeats[Caenorhabditis elegansDII   
 2004.96.7.1      
35781 2004.171.6.1 ci0100151338 gi|12644578|sp|Q9I8B0|SUR6_XENLA Surfeit locus protein 6 homologue [Xenopus laevisDI   
 2005.171.6.1      
22776 2004.342.4.1 ci0100136887 IPI:IPI00110325.1|NP_075359|TREMBL:Q9EQ 31|Lysophosphatidic acid receptor [Homo sapiens  
43913 2005.342.5.1      
34161 2004.269.19.1 ci0100151642 No hit found DII   
 2005.269.28.1      
8523 2004.9.52.1 ci0100149839 gi|7799191|emb|CAB90827.1|tomoregulin-1 [Mus musculus] (Ci-tomoregulin  
 2005.9.53.1      
43089 2004.780.6.1 ci0100133150 IPI:IPI00002502.1| NP_001665| Cyclic-AMP-dependent transcription factor ATF-3 [Homo sapiens  
9784 2005.780.10.1      
33082       
41212 2005.492.2.1 ci0100150570 gi|15623822|dbj|BAB67881.1| hypothetical protein~similar to Arabidopsis thaliana chromosome 3, T22E16.10[Oryza sativaDI   
18277 2004.224.7.1 ci0100152617 gi|3694666|gb|AAC62435.1| ETS-related transcription factor (binds CGGAW) [Homo sapiens](Ci-ETS  
38399 2005.224.5.1      
34792 No model found No model found LEM3-human P selectin precursor (Ci-Sccpa(Davidson and Swalla, 2002) Papilla (Davidson and Swalla,2002) 
19963 2004.546.7.1 ci0100146623 Q9VQA9 (Q9VQA9) CG15388 protein [Drosophila melanogasterDI   
 2005.546.7.1      
8514 2004.179.6.1 ci0100143863 gi|16156758|dbj|BAB62269.1| HrPost-1[Halocynthia roretzi]; 0006886, intracellular protein transport (Davidson and Swalla, 2002)  
 2005.179.6.1      
3279 2004.1.165.1 ci0100148521 gi|19697349|gb|AAL92989.1| hypothetical protein[Dictyostelium discoideumDI   
 2005.1.179.1      
10655 2004.148.20.1 ci0100143927 gi|1110451|dbj|BAA08728.1| HrHox-1[Halocynthia roretzi  
23352 2005.148.22.1      
10654       
25668       
42958       
10653       
24373 2004.86.21.1 ci0100139734 No hit found DII   
 2005.86.21.1      
34078 2004.129.22.1 ci0100132083 gi|10441571|gb|AAG17109.1| P2.6 melatonin receptor Mel-1B [Esox lucius]; 0007186, G-protein coupled receptor protein signalling pathway   
 2005.129.20.1      
33654 2004.145.2.1 ci0100133750 gi|18549022|ref|XP_059205.2| similar to RIKEN cDNA 2810004N23 [Homo sapiensDI   
 2005.145.2.1      
43630 2004.88.19.1 ci0100143297 gi|14994043|gb|AAK76396.1| Rev-Erb beta 2[Danio rerio]; 0003707, steroid hormone receptor activity(Ci-Rev-erb Palps (Kusakabet et al., 2002) 
31284 2005.88.22.1      
22053 2004.27.26.1 ci0100142399 IPI:IPI00128222.1|ENSEMBL:ENSMUSP00000 037887 [Homo sapiensDI   
 2004.27.26.2      
 2005.27.28.1      
 2005.27.28.2      
19227 2005.1063.1.1 ci0100130992 Gi|20890036|ref|XP8129286.1| Similar to RRP5 protein homologue [Mus musculusDII   
 2004.1063.1.1      
16998 2004.62.15.1 ci0100148566 IPI:IPI00132628.1|ENSEMBL:ENSMUSP00000 046720) [Homo sapiensDI   
 2005.62.15.1      
39245 2004.168.9.1 ci0100130565 IPI:IPI00166146.1|TREMBL:Q8N1E9| Similar to selectin P [Homo sapiens] (Ci-Sccpb(Davidson and Swalla, 2002) Papilla (Davidson and Swalla,2002) 
 2005.168.9.1      
21530 2004.14.52.1 ci0100148511 IPI:IPI00029521.4 NTKL-Binding protein I (Ci-NTKLDI   
 2005.14.53.1      
37229 2004.102.45.1 ci0100134538 Q9VHK5 (Q9VHK5) CG8379 protein (LD21733p) [Drosophila melanogasterDI   
 2005.102.59.1      
12589 2004.22.90.1 ci0100143826 hsa:79987 POLYDOM; probable orthologue of mouse polydom [Homo sapiens  
28225 2005.22.85.1      
2772 2004.409.5.1 ci0100130842 mmu:73690 2410114O14Rik; RIKEN cDNA 2410114O14 gene [Mus musculus];0005576, extracellular; Defense-related protein containing SCP domain. (Davidson and Swalla, 2002)  
 2005.409.5.1      
31955 2004.1460.1.1 ci0100141080 hsa:10352 WARS2; tryptophanyl tRNA synthetase 2 (mitochondrial) [Homo sapiens(Woods et al., 2004)  
 2005.1460.1.1      
34464 2004.229.19.1 ci0100133625 IPI:IPI00117008.1|ENSEMBL:ENSMUSP00000 028486 [Homo sapiensDI   
6947 2005.229.21.1      
43522 No model found ci0100132461 IPI:IPI00016046.1|REFSEQ_NP:NP_542786Pr otein c20orf52 [Homo sapiensDI   
2255 2004.1067.1.1 ci0100150638 No hit found DII   
 2005.1067.2.1      
5797 2005.31.74.1 ci0100134193 IPI:IPI00028491.3| XP_005298|1-acyl-snglycerol-3-phosphate acyltransferase epsilon [Homo sapiens  
7913 2004.49.39.1 ci0100140291 gi|11527806|dbj|BAB 18672.1| fucosyltransferase[Pongo pygmaeus  
 2005.49.45.1      
Genes downregulated by U0126 treatment
Chip featureKyotoGrail gene modelJGI version 1 gene modelIdentityClassReferences*In situ
21484 2004.18.40.1 ci0100145332 NM112885 protein binding/ubiquitin protein ligase/Zn-ion binding[Arabidopsis thalianaDI   
28505 2004.18.40.2      
 2005.18.42.1      
 2005.18.42.2      
40650 2004.132.46.1 No model found Rat nuclear pore complex N153 (Nup 153) sp:P49791   
 2005.132.44.1      
10051 2004.43.38.1 ci0100148033 O61785 (O61785) Hypothetical 29.0 kDa protein [Caenorhabditis elegansDI   
 2005.43.38.1      
19579 2004.58.13.1 ci0100131282 gi|19032245|emb|CAD24308.1| putative coagulation serine protease [Ciona intestinalis(Davidson and Swalla, 2002)  
 2005.58.13.1      
20246 2004.305.11.1 ci0100149359 IPI:IPI00001729 Matrix metalloprotease-24-precursor (Ci-Mx  
30477 2005.305.12.1      
14883 2004.82.31.1 ci0100147945 IPI:IPI00112858.1|NP_073725| Polydom protein precursor [Homo sapiens] (Ci-polydom  
 2005.82.27.1      
 2005.82.27.2      
 2005.82.27.3      
41165 2004.18.53.1 ci0100146122 gi|4468715|emb|CAB38105.1| beta-microseminoprotein[Saguinus oedipusDI   
 2005.18.55.1      
33659 2004.163.38.1 ci0100139661 gi|12381859|dbj|BAB21104.2| SMaf1 [Danio rerio]. 0006355, regulation of transcription, DNA-dependent   
25306 2005.163.33.1      
6228       
23758 2004.272.9.1 ci0100141699 No hit found DII   
2153 2005.272.10.1      
10333 2004.51.20.1 ci0100154804 IPI:IPI00165235.1| Similar to carboxypeptidase Z [Homo sapiens] (Ci-carboxypeptidase(Nakayama et al., 2001)(Nakayama et al., 2002)  
39015 2005.51.23.1      
20529       
41121       
29978 2005.96.7.1 ci0100141212 gi|17538868|ref|NP_502249.1|ankyrin repeats[Caenorhabditis elegansDII   
 2004.96.7.1      
35781 2004.171.6.1 ci0100151338 gi|12644578|sp|Q9I8B0|SUR6_XENLA Surfeit locus protein 6 homologue [Xenopus laevisDI   
 2005.171.6.1      
22776 2004.342.4.1 ci0100136887 IPI:IPI00110325.1|NP_075359|TREMBL:Q9EQ 31|Lysophosphatidic acid receptor [Homo sapiens  
43913 2005.342.5.1      
34161 2004.269.19.1 ci0100151642 No hit found DII   
 2005.269.28.1      
8523 2004.9.52.1 ci0100149839 gi|7799191|emb|CAB90827.1|tomoregulin-1 [Mus musculus] (Ci-tomoregulin  
 2005.9.53.1      
43089 2004.780.6.1 ci0100133150 IPI:IPI00002502.1| NP_001665| Cyclic-AMP-dependent transcription factor ATF-3 [Homo sapiens  
9784 2005.780.10.1      
33082       
41212 2005.492.2.1 ci0100150570 gi|15623822|dbj|BAB67881.1| hypothetical protein~similar to Arabidopsis thaliana chromosome 3, T22E16.10[Oryza sativaDI   
18277 2004.224.7.1 ci0100152617 gi|3694666|gb|AAC62435.1| ETS-related transcription factor (binds CGGAW) [Homo sapiens](Ci-ETS  
38399 2005.224.5.1      
34792 No model found No model found LEM3-human P selectin precursor (Ci-Sccpa(Davidson and Swalla, 2002) Papilla (Davidson and Swalla,2002) 
19963 2004.546.7.1 ci0100146623 Q9VQA9 (Q9VQA9) CG15388 protein [Drosophila melanogasterDI   
 2005.546.7.1      
8514 2004.179.6.1 ci0100143863 gi|16156758|dbj|BAB62269.1| HrPost-1[Halocynthia roretzi]; 0006886, intracellular protein transport (Davidson and Swalla, 2002)  
 2005.179.6.1      
3279 2004.1.165.1 ci0100148521 gi|19697349|gb|AAL92989.1| hypothetical protein[Dictyostelium discoideumDI   
 2005.1.179.1      
10655 2004.148.20.1 ci0100143927 gi|1110451|dbj|BAA08728.1| HrHox-1[Halocynthia roretzi  
23352 2005.148.22.1      
10654       
25668       
42958       
10653       
24373 2004.86.21.1 ci0100139734 No hit found DII   
 2005.86.21.1      
34078 2004.129.22.1 ci0100132083 gi|10441571|gb|AAG17109.1| P2.6 melatonin receptor Mel-1B [Esox lucius]; 0007186, G-protein coupled receptor protein signalling pathway   
 2005.129.20.1      
33654 2004.145.2.1 ci0100133750 gi|18549022|ref|XP_059205.2| similar to RIKEN cDNA 2810004N23 [Homo sapiensDI   
 2005.145.2.1      
43630 2004.88.19.1 ci0100143297 gi|14994043|gb|AAK76396.1| Rev-Erb beta 2[Danio rerio]; 0003707, steroid hormone receptor activity(Ci-Rev-erb Palps (Kusakabet et al., 2002) 
31284 2005.88.22.1      
22053 2004.27.26.1 ci0100142399 IPI:IPI00128222.1|ENSEMBL:ENSMUSP00000 037887 [Homo sapiensDI   
 2004.27.26.2      
 2005.27.28.1      
 2005.27.28.2      
19227 2005.1063.1.1 ci0100130992 Gi|20890036|ref|XP8129286.1| Similar to RRP5 protein homologue [Mus musculusDII   
 2004.1063.1.1      
16998 2004.62.15.1 ci0100148566 IPI:IPI00132628.1|ENSEMBL:ENSMUSP00000 046720) [Homo sapiensDI   
 2005.62.15.1      
39245 2004.168.9.1 ci0100130565 IPI:IPI00166146.1|TREMBL:Q8N1E9| Similar to selectin P [Homo sapiens] (Ci-Sccpb(Davidson and Swalla, 2002) Papilla (Davidson and Swalla,2002) 
 2005.168.9.1      
21530 2004.14.52.1 ci0100148511 IPI:IPI00029521.4 NTKL-Binding protein I (Ci-NTKLDI   
 2005.14.53.1      
37229 2004.102.45.1 ci0100134538 Q9VHK5 (Q9VHK5) CG8379 protein (LD21733p) [Drosophila melanogasterDI   
 2005.102.59.1      
12589 2004.22.90.1 ci0100143826 hsa:79987 POLYDOM; probable orthologue of mouse polydom [Homo sapiens  
28225 2005.22.85.1      
2772 2004.409.5.1 ci0100130842 mmu:73690 2410114O14Rik; RIKEN cDNA 2410114O14 gene [Mus musculus];0005576, extracellular; Defense-related protein containing SCP domain. (Davidson and Swalla, 2002)  
 2005.409.5.1      
31955 2004.1460.1.1 ci0100141080 hsa:10352 WARS2; tryptophanyl tRNA synthetase 2 (mitochondrial) [Homo sapiens(Woods et al., 2004)  
 2005.1460.1.1      
34464 2004.229.19.1 ci0100133625 IPI:IPI00117008.1|ENSEMBL:ENSMUSP00000 028486 [Homo sapiensDI   
6947 2005.229.21.1      
43522 No model found ci0100132461 IPI:IPI00016046.1|REFSEQ_NP:NP_542786Pr otein c20orf52 [Homo sapiensDI   
2255 2004.1067.1.1 ci0100150638 No hit found DII   
 2005.1067.2.1      
5797 2005.31.74.1 ci0100134193 IPI:IPI00028491.3| XP_005298|1-acyl-snglycerol-3-phosphate acyltransferase epsilon [Homo sapiens  
7913 2004.49.39.1 ci0100140291 gi|11527806|dbj|BAB 18672.1| fucosyltransferase[Pongo pygmaeus  
 2005.49.45.1      

Identification of genes under the control of the ERK pathway. See legend to Table 1.

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