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Expression of 1-1-2.1.20.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92312	0.617
27DAP/17DAP	0.74072	0.496
39DAP/27DAP	1.27388	0.735
41DAP/39DAP	0.96904	0.887
42DAP/41DAP	1.04398	0.992
43DAP/42DAP	1.13274	1
47DAP/43DAP	2.0691	0.195
52DAP/47DAP	0.93849	0.783
57DAP/52DAP	1.45208	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93322	0.103
17DAP/reference	1.01104	0.653
27DAP/reference	1.04901	0.623
39DAP/reference	1.08229	0.031
41DAP/reference	1.0109	0.855
42DAP/reference	0.94525	0.145
43DAP/reference	1.03175	0.758
47DAP/reference	0.99368	0.602
52DAP/reference	1.14372	0.302
57DAP/reference	1.07223	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94671	0.526
27DAP/17DAP	0.93986	0.648
39DAP/27DAP	1.17087	0.173
41DAP/39DAP	1.06559	0.88
42DAP/41DAP	0.97997	0.781
43DAP/42DAP	1.04877	0.351
47DAP/43DAP	1.0115	0.956
52DAP/47DAP	1.09343	0.66
57DAP/52DAP	1.05108	0.832
57DAP/7DAP	1.04839	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83698	0.066
17DAP/reference	0.89124	0.049
27DAP/reference	1.12432	0.131
39DAP/reference	0.84447	0.034
41DAP/reference	0.8661	0.044
42DAP/reference	0.83375	0.017
43DAP/reference	0.75704	0.011
47DAP/reference	0.87562	0.222
52DAP/reference	0.79697	0.018
57DAP/reference	0.86758	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89198	0.032
17DAP/reference	0.80839	0.019
27DAP/reference	0.87456	0.173
39DAP/reference	0.8789	0.156
41DAP/reference	1.08699	0.831
42DAP/reference	1.00298	0.723
43DAP/reference	1.2449	0.23
47DAP/reference	1.03581	0.388
52DAP/reference	0.9236	0.043
57DAP/reference	0.86369	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83553	0.059
17DAP/reference	0.95765	0.426
27DAP/reference	1.00017	0.883
39DAP/reference	0.90442	0.076
41DAP/reference	1.05488	0.411
42DAP/reference	0.99035	0.816
43DAP/reference	0.85849	0.027
47DAP/reference	0.9775	0.452
52DAP/reference	0.91939	0.351
57DAP/reference	0.94523	0.326

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00686	0.966
26DAP/20DAP	0.93725	1
34DAP/26DAP	1.07365	1
51DAP/34DAP	1.09313	0.775
52DAP/51DAP	0.94348	1
53DAP/52DAP	1.06272	0.712
55DAP/53DAP	1.15286	0.355
57DAP/55DAP	0.99857	0.925
62DAP/57DAP	0.91546	0.871
68DAP/62DAP	1.40157	0.582
68DAP/14DAP	1.15897	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92268	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.16982	0.666
Mature Green Tomato/Ripe Tomato	0.1778	0.017
Immature Eggplant/Mature Eggplant	0.93095	0.808
Ripe Pepper/Ripe Tomato	0.41033	0.224
Mature Eggplant/Ripe Tomato	0.64932	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.75401	N/A
1-1-2/M82	0.99752	1
12-2/M82	N/A	N/A
12-4/M82	1.05051	0.611
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.00622	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.96575	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.90826	1
6-2/M82	N/A	N/A
6-3/M82	1.0298	N/A
7-1/M82	1.0452	1
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.41743	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.69348	0.559
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.2102	1
WT/WTpooled	N/A	N/A

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	0.77744	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99573	1
DC3000/delta hrp 6h	0.87856	0.95
DC3000/delta hrp 12h	0.93798	1
DC3000/delta hrp 24h	0.96603	0.794

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1922	0.25
DC3000 delta B/DC3000 delta AB	1.08193	0.443

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08401	1
Exp 36h	1.12946	1
Exp 60h	0.96084	0.522

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	1.00755	1
Var 12h NI row2-row1	0.9214	0.627
Var 36h I row2-row1	1.07705	1
Var 36h NI row2-row1	1.296	1
Var 60h I row2-row1	0.82702	N/A
Var 60h NI row2-row1	0.98998	1
Time course 0hI-0hNI	1.01387	0.867
Time course 12hI-12hNI	0.8632	0.446
Time course 36hI-36hNI	1.03334	0.742
Time course 60hI-60hNI	1.59738	0.137

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)	0.99754	0.931
transgenic ySAMdc/azygous control (breaker)	1.30022	0.172
transgenic ySAMdc/azygous control (red)	1.02329	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00109	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9894	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0332	1
Manapal/WT (break)	0.96867	1
Manapal/WT (red)	0.65892	0.181