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Expression of 1-1-2.1.11.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9392	0.578
27DAP/17DAP	1.06584	1
39DAP/27DAP	0.80388	0.382
41DAP/39DAP	1.11097	0.806
42DAP/41DAP	1.10888	0.958
43DAP/42DAP	1.10026	1
47DAP/43DAP	1.74152	0.277
52DAP/47DAP	1.10035	0.973
57DAP/52DAP	1.30449	0.565

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93803	0.371
17DAP/reference	1.12417	0.294
27DAP/reference	0.90202	0.17
39DAP/reference	1.10658	0.403
41DAP/reference	1.10141	0.451
42DAP/reference	0.83093	0.002
43DAP/reference	0.99696	0.84
47DAP/reference	0.86899	0.046
52DAP/reference	0.8495	0.075
57DAP/reference	0.92372	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77875	0.135
27DAP/17DAP	0.88876	0.684
39DAP/27DAP	1.07469	0.471
41DAP/39DAP	0.8369	0.446
42DAP/41DAP	1.11047	0.719
43DAP/42DAP	0.9267	0.729
47DAP/43DAP	1.11244	0.892
52DAP/47DAP	1.14487	0.619
57DAP/52DAP	1.00177	0.828
57DAP/7DAP	1.06833	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00376	1
17DAP/reference	1.35499	0.023
27DAP/reference	1.23534	0.011
39DAP/reference	1.32033	0.03
41DAP/reference	1.27468	0.184
42DAP/reference	1.24473	0.037
43DAP/reference	1.37533	0.048
47DAP/reference	0.97469	0.671
52DAP/reference	1.15798	0.308
57DAP/reference	1.20645	0.108

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98832	0.848
17DAP/reference	0.95432	0.536
27DAP/reference	0.97036	0.452
39DAP/reference	1.072	1
41DAP/reference	0.79692	0.049
42DAP/reference	0.86767	0.237
43DAP/reference	1.39241	0.144
47DAP/reference	0.89179	0.302
52DAP/reference	0.7801	0.101
57DAP/reference	0.88831	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08393	0.408
17DAP/reference	1.14092	0.585
27DAP/reference	1.60164	0.015
39DAP/reference	1.32415	0.052
41DAP/reference	1.28842	0.02
42DAP/reference	1.3493	0.251
43DAP/reference	1.18225	0.547
47DAP/reference	1.01685	1
52DAP/reference	1.38698	0.377
57DAP/reference	0.77466	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03271	1
26DAP/20DAP	1.51067	0.534
34DAP/26DAP	1.29266	1
51DAP/34DAP	1.16333	0.281
52DAP/51DAP	0.67243	1
53DAP/52DAP	0.80845	0.133
55DAP/53DAP	0.9078	0.698
57DAP/55DAP	0.93918	0.799
62DAP/57DAP	1.01636	1
68DAP/62DAP	1.22866	0.931
68DAP/14DAP	1.85296	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77611	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.25673	0.089
Mature Green Tomato/Ripe Tomato	1.36799	0.185
Immature Eggplant/Mature Eggplant	0.87479	0.448
Ripe Pepper/Ripe Tomato	2.4336	0.256
Mature Eggplant/Ripe Tomato	0.8951	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.144	N/A
1-1-2/M82	1.26157	1
12-2/M82	N/A	N/A
12-4/M82	1.00858	1
1-3/M82	N/A	N/A
2-1-1/M82	1.38347	N/A
2-1/M82	N/A	N/A
2-6/M82	0.98791	1
3-2/M82	1.09753	N/A
4-1-1/M82	1.33005	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.20686	N/A
4-3/M82	1.07834	1
5-3/M82	1.10442	1
6-2/M82	N/A	N/A
6-3/M82	0.89125	1
7-1/M82	1.19483	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.23143	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93675	1
IL2-6/WTpooled	0.69391	0.473
IL7-5/WTpooled	0.69201	N/A
IL7-3/WTpooled	0.97468	1
IL12-4/WTpooled	0.82973	0.566
IL1-4/WTpooled	0.92574	0.834
WT/WTpooled	1.10085	0.855

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	0.90704	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07962	0.921
DC3000/delta hrp 6h	0.75529	0.95
DC3000/delta hrp 12h	0.99426	1
DC3000/delta hrp 24h	1.11577	0.453

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	N/A	N/A
Exp 36h	1.03586	1
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01228	1
Var 0h	0.82813	0.196
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	0.89232	0.438
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.44543	0.904
Time course 0hI-0hNI	0.921	0.634
Time course 12hI-12hNI	0.89482	0.687
Time course 36hI-36hNI	0.78294	0.111
Time course 60hI-60hNI	0.59403	0.008

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)	1.11051	0.305
transgenic ySAMdc/azygous control (breaker)	0.75193	0.134
transgenic ySAMdc/azygous control (red)	1.08177	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99743	0.886

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.52014	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.65715	0.172
Manapal/WT (break)	0.80231	1
Manapal/WT (red)	1.14867	0.137