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Expression of 1-1-2.2.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04877	0.838
27DAP/17DAP	1.0028	1
39DAP/27DAP	1.13823	0.681
41DAP/39DAP	1.00107	1
42DAP/41DAP	0.96456	1
43DAP/42DAP	0.95047	0.773
47DAP/43DAP	0.96274	0.851
52DAP/47DAP	1.24708	0.516
57DAP/52DAP	1.03989	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11717	0.265
17DAP/reference	0.9643	0.26
27DAP/reference	1.00705	0.863
39DAP/reference	0.9652	0.284
41DAP/reference	0.95636	0.201
42DAP/reference	1.06064	0.004
43DAP/reference	0.99947	0.942
47DAP/reference	1.05801	0.105
52DAP/reference	1.04423	0.43
57DAP/reference	1.07353	0.202

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02118	0.774
27DAP/17DAP	0.87363	0.295
39DAP/27DAP	1.06246	0.514
41DAP/39DAP	1.00917	0.914
42DAP/41DAP	1.03171	0.836
43DAP/42DAP	0.99619	1
47DAP/43DAP	0.99067	0.954
52DAP/47DAP	0.93226	0.719
57DAP/52DAP	1.02457	0.891
57DAP/7DAP	0.98268	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05929	0.732
17DAP/reference	1.1226	0.025
27DAP/reference	1.16043	0.041
39DAP/reference	1.01484	1
41DAP/reference	1.05833	0.402
42DAP/reference	1.03648	0.233
43DAP/reference	1.17021	0.386
47DAP/reference	1.19513	0.386
52DAP/reference	1.51194	0.459
57DAP/reference	1.09064	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00512	0.885
17DAP/reference	1.02435	0.543
27DAP/reference	1.07547	0.283
39DAP/reference	1.07102	0.263
41DAP/reference	0.97766	0.451
42DAP/reference	1.06188	0.359
43DAP/reference	0.98806	0.721
47DAP/reference	0.94177	0.129
52DAP/reference	1.01548	0.667
57DAP/reference	1.00546	0.98

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01144	N/A
17DAP/reference	1.07808	0.538
27DAP/reference	1.30346	0.038
39DAP/reference	1.32162	0.037
41DAP/reference	1.14194	0.054
42DAP/reference	1.15483	0.327
43DAP/reference	1.12986	0.275
47DAP/reference	0.9579	0.215
52DAP/reference	1.06686	0.614
57DAP/reference	1.20693	0.086

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96248	1
26DAP/20DAP	1.092	0.7
34DAP/26DAP	1.05812	1
51DAP/34DAP	1.0584	0.402
52DAP/51DAP	1.04059	0.689
53DAP/52DAP	0.73347	N/A
55DAP/53DAP	1.16319	0.375
57DAP/55DAP	1.00579	0.997
62DAP/57DAP	0.92757	0.871
68DAP/62DAP	0.80172	0.144
68DAP/14DAP	0.86879	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0654	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.41336	0.058
Mature Green Tomato/Ripe Tomato	1.06056	0.752
Immature Eggplant/Mature Eggplant	1.10078	0.334
Ripe Pepper/Ripe Tomato	1.40796	0.256
Mature Eggplant/Ripe Tomato	1.8581	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79494	0.613
1-1-2/M82	0.87413	1
12-2/M82	0.71383	N/A
12-4/M82	0.96044	0.358
1-3/M82	0.98907	1
2-1-1/M82	1.0438	N/A
2-1/M82	0.98208	N/A
2-6/M82	0.83143	1
3-2/M82	1.07917	0.426
4-1-1/M82	N/A	N/A
4-1/M82	0.95211	1
4-3-2/M82	0.70598	0.487
4-3/M82	N/A	N/A
5-3/M82	0.97461	1
6-2/M82	1.04017	N/A
6-3/M82	N/A	N/A
7-1/M82	1.04645	N/A
7-2/M82	0.86886	N/A
9-3-2/M82	0.78561	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.25958	0.277
IL2-6/WTpooled	1.13667	0.584
IL7-5/WTpooled	1.07117	1
IL7-3/WTpooled	0.87137	0.31
IL12-4/WTpooled	1.14305	0.891
IL1-4/WTpooled	1.01331	1
WT/WTpooled	0.91766	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	0.98711	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.943	1
DC3000/delta hrp 6h	0.95357	0.95
DC3000/delta hrp 12h	1.04073	1
DC3000/delta hrp 24h	1.05017	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.52249	0.042
DC3000 delta B/DC3000 delta AB	1.38249	0.133

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21483	1
Exp 36h	1.2694	1
Exp 60h	1.2377	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00026	1
Var 0h	0.99908	1
Var 12h I row2-row1	1.23277	0.204
Var 12h NI row2-row1	1.00239	1
Var 36h I row2-row1	1.14908	1
Var 36h NI row2-row1	0.9628	0.743
Var 60h I row2-row1	1.09601	1
Var 60h NI row2-row1	1.06198	1
Time course 0hI-0hNI	1.0051	1
Time course 12hI-12hNI	1.00143	1
Time course 36hI-36hNI	1.02455	0.453
Time course 60hI-60hNI	1.81995	0.012

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)	0.92728	0.614
transgenic ySAMdc/azygous control (breaker)	1.09201	1
transgenic ySAMdc/azygous control (red)	1.03689	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96931	0.093

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.14532	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87914	1
Manapal/WT (break)	0.91046	0.333
Manapal/WT (red)	3.42989	0.15