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Expression of 1-1-3.3.20.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20274	0.602
27DAP/17DAP	1.46996	0.552
39DAP/27DAP	1.02159	0.798
41DAP/39DAP	1.05455	0.964
42DAP/41DAP	1.1997	0.709
43DAP/42DAP	1.16588	0.835
47DAP/43DAP	1.30432	0.618
52DAP/47DAP	0.69495	0.297
57DAP/52DAP	1.13168	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81024	0.035
17DAP/reference	0.78691	0.016
27DAP/reference	0.97739	0.683
39DAP/reference	0.86139	0.106
41DAP/reference	0.7979	0.018
42DAP/reference	0.8331	0.004
43DAP/reference	0.98275	0.675
47DAP/reference	0.96997	0.345
52DAP/reference	1.0752	0.663
57DAP/reference	1.03775	0.478

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95468	0.679
27DAP/17DAP	0.97193	0.919
39DAP/27DAP	1.0709	0.854
41DAP/39DAP	1.30167	0.887
42DAP/41DAP	1.09634	1
43DAP/42DAP	0.89556	0.801
47DAP/43DAP	0.94577	0.939
52DAP/47DAP	1.13563	0.856
57DAP/52DAP	1.83117	0.135
57DAP/7DAP	0.92644	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24207	0.16
17DAP/reference	1.4596	0.007
27DAP/reference	1.14357	0.371
39DAP/reference	1.58911	0.009
41DAP/reference	1.35827	0.048
42DAP/reference	1.43798	0.007
43DAP/reference	1.28696	0.511
47DAP/reference	1.20884	0.318
52DAP/reference	1.17944	0.212
57DAP/reference	1.24396	0.082

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7571	0.007
17DAP/reference	0.6694	0.004
27DAP/reference	0.81816	0.069
39DAP/reference	0.77367	0.022
41DAP/reference	0.96136	0.364
42DAP/reference	0.86178	0.023
43DAP/reference	0.76752	0.019
47DAP/reference	0.83265	0.019
52DAP/reference	0.848	0.008
57DAP/reference	0.75936	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13414	0.723
17DAP/reference	0.98518	0.709
27DAP/reference	1.22781	0.034
39DAP/reference	1.22614	0.045
41DAP/reference	1.07984	0.383
42DAP/reference	1.0192	1
43DAP/reference	0.90112	0.226
47DAP/reference	1.00668	1
52DAP/reference	1.381	0.241
57DAP/reference	1.07771	0.771

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19329	0.966
26DAP/20DAP	1.00852	1
34DAP/26DAP	1.2906	1
51DAP/34DAP	N/A	N/A
52DAP/51DAP	1.42452	N/A
53DAP/52DAP	1.04916	0.91
55DAP/53DAP	1.0563	0.719
57DAP/55DAP	1.01632	0.888
62DAP/57DAP	1.1603	0.445
68DAP/62DAP	1.12102	0.944
68DAP/14DAP	1.21899	0.615

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23056	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27169	N/A
Mature Green Tomato/Ripe Tomato	0.72862	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	4.58602	0.235
Mature Eggplant/Ripe Tomato	0.95746	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95908	0.883
1-1-2/M82	0.94932	0.958
12-2/M82	N/A	N/A
12-4/M82	1.05729	1
1-3/M82	0.64348	N/A
2-1-1/M82	1.35971	0.3
2-1/M82	N/A	N/A
2-6/M82	1.05675	0.425
3-2/M82	N/A	N/A
4-1-1/M82	1.18271	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.6977	N/A
5-3/M82	0.95042	1
6-2/M82	0.92561	N/A
6-3/M82	1.20903	N/A
7-1/M82	N/A	N/A
7-2/M82	1.03732	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.65232	0.247
IL2-6/WTpooled	1.12523	0.659
IL7-5/WTpooled	0.98644	1
IL7-3/WTpooled	1.03811	1
IL12-4/WTpooled	1.08789	0.891
IL1-4/WTpooled	0.97207	0.699
WT/WTpooled	1.02028	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.76805	0.497

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02813	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.21744	1
DC3000/delta hrp 24h	0.82938	0.05

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.75025	1
Exp 36h	0.94176	0.879
Exp 60h	1.16367	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	1.42137	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.99102	0.904
Time course 0hI-0hNI	0.95678	0.942
Time course 12hI-12hNI	2.10559	0.56
Time course 36hI-36hNI	0.83185	0.306
Time course 60hI-60hNI	5.33234	0.022

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.97737	0.789
transgenic ySAMdc/azygous control (breaker)	0.92142	0.49
transgenic ySAMdc/azygous control (red)	0.68324	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17332	0.032

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86485	0.284

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92067	1
Manapal/WT (break)	1.17419	0.381
Manapal/WT (red)	0.84074	0.36