Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.4.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02895	0.977
27DAP/17DAP	1.21814	0.86
39DAP/27DAP	1.07643	1
41DAP/39DAP	1.37023	0.408
42DAP/41DAP	0.90635	1
43DAP/42DAP	0.84324	0.583
47DAP/43DAP	0.95724	0.815
52DAP/47DAP	1.38314	0.346
57DAP/52DAP	0.98642	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04095	0.735
17DAP/reference	0.95242	0.194
27DAP/reference	0.98701	0.683
39DAP/reference	0.99496	0.957
41DAP/reference	1.0135	0.808
42DAP/reference	1.00161	0.731
43DAP/reference	0.9866	0.745
47DAP/reference	0.95636	0.065
52DAP/reference	1.09503	0.256
57DAP/reference	0.90899	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	2.53734
39DAP/27DAP	1.18597	0.854
41DAP/39DAP	1.81529	0.347
42DAP/41DAP	1.43438	1
43DAP/42DAP	0.58638
47DAP/43DAP	N/A	N/A
52DAP/47DAP	1.1479	0.8
57DAP/52DAP	1.84368
57DAP/7DAP	2.15143

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96083	0.361
17DAP/reference	0.9524	0.012
27DAP/reference	0.89806	0.01
39DAP/reference	0.92741	0.015
41DAP/reference	0.93495	0.049
42DAP/reference	0.92884	0.032
43DAP/reference	1.16169	0.923
47DAP/reference	0.88027	0.066
52DAP/reference	0.87436	0.027
57DAP/reference	0.91626	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0264	0.589
17DAP/reference	1.00517	0.924
27DAP/reference	1.06665	0.38
39DAP/reference	0.97923	0.554
41DAP/reference	0.82742	0.307
42DAP/reference	1.0496	0.715
43DAP/reference	1.10958	0.112
47DAP/reference	0.90834	0.029
52DAP/reference	0.93397	0.093
57DAP/reference	1.05573	0.908

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99807	0.804
17DAP/reference	1.04835	0.248
27DAP/reference	1.01817	0.695
39DAP/reference	1.00466	0.912
41DAP/reference	0.95938	0.237
42DAP/reference	0.95531	0.361
43DAP/reference	0.98313	0.503
47DAP/reference	0.98821	0.593
52DAP/reference	0.95204	0.529
57DAP/reference	0.84529	0.037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96334	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.6395	1
51DAP/34DAP	0.8376	0.606
52DAP/51DAP	1.2748	0.08
53DAP/52DAP	0.66794	0.402
55DAP/53DAP	0.90738	0.675
57DAP/55DAP	0.96236
62DAP/57DAP	1.06795	0.35
68DAP/62DAP	0.96153	0.81
68DAP/14DAP	1.10113	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.36841

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.60342	0.154
Mature Green Tomato/Ripe Tomato	0.79038	0.042
Immature Eggplant/Mature Eggplant	1.04829	0.462
Ripe Pepper/Ripe Tomato	3.08935	1
Mature Eggplant/Ripe Tomato	1.55453	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97956	0.944
1-1-2/M82	0.83899	1
12-2/M82	0.99932	1
12-4/M82	1.05895	1
1-3/M82	0.96433	0.441
2-1-1/M82	1.04474	0.764
2-1/M82	N/A	N/A
2-6/M82	0.9666	1
3-2/M82	0.97112	1
4-1-1/M82	1.03376	1
4-1/M82	0.97769	1
4-3-2/M82	0.99631	1
4-3/M82	0.95304	0.72
5-3/M82	0.99886	1
6-2/M82	1.04611	1
6-3/M82	0.98324	1
7-1/M82	0.96407	1
7-2/M82	0.94673	0.599
9-3-2/M82	0.93881	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.7926	0.581
IL1-4/WTpooled	0.98728	1
WT/WTpooled	1.11917	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07539	0.774
DC3000/delta hrp 6h	0.89258	0.95
DC3000/delta hrp 12h	1.0499	1
DC3000/delta hrp 24h	1.02199	0.728

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	1.20296	1
Exp 36h	0.80589	0.699
Exp 60h	0.73597	0.664

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	1.13838	0.594
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	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.91081	0.314
transgenic ySAMdc/azygous control (breaker)	1.21293	0.166
transgenic ySAMdc/azygous control (red)	0.92287	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06636	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23721	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.45576	0.105
Manapal/WT (break)	1.15812	1
Manapal/WT (red)	1.78952	0.137