Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.58916	0.015
27DAP/17DAP	0.95587	0.939
39DAP/27DAP	1.09519	0.946
41DAP/39DAP	0.93942	0.772
42DAP/41DAP	1.03565	1
43DAP/42DAP	1.00952	0.937
47DAP/43DAP	1.21434	0.756
52DAP/47DAP	0.989	0.856
57DAP/52DAP	0.93963	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71192	0.033
17DAP/reference	0.56096	0.009
27DAP/reference	1.00862	0.725
39DAP/reference	0.76866	0.076
41DAP/reference	0.56232	0.018
42DAP/reference	1.17861	0.338
43DAP/reference	1.19605	0.102
47DAP/reference	1.54334	0.032
52DAP/reference	1.93267	0.013
57DAP/reference	2.35545	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84744	0.363
27DAP/17DAP	0.80072	0.782
39DAP/27DAP	0.87831	0.529
41DAP/39DAP	0.98116	0.959
42DAP/41DAP	0.69556	0.037
43DAP/42DAP	1.32812	0.134
47DAP/43DAP	1.08232	0.973
52DAP/47DAP	1.29368	0.492
57DAP/52DAP	0.81789	0.354
57DAP/7DAP	0.9569

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38295	0.036
17DAP/reference	1.32839	0.007
27DAP/reference	1.251	0.023
39DAP/reference	1.23386	0.028
41DAP/reference	1.49265	0.008
42DAP/reference	1.36625	0.007
43DAP/reference	1.42763	0.01
47DAP/reference	1.74795	0.014
52DAP/reference	1.50547	0.008
57DAP/reference	1.30286	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74089	0.087
17DAP/reference	0.57125	0.007
27DAP/reference	1.03335	0.711
39DAP/reference	1.30798	0.255
41DAP/reference	1.83152	0.005
42DAP/reference	1.35623	0.008
43DAP/reference	0.71166	0.09
47DAP/reference	1.27669	0.013
52DAP/reference	1.13326	0.3
57DAP/reference	0.8722	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32801	0.386
17DAP/reference	0.9454	0.56
27DAP/reference	1.20111	0.137
39DAP/reference	1.17722	0.264
41DAP/reference	1.13644	0.276
42DAP/reference	1.58268	0.034
43DAP/reference	1.81324	0.021
47DAP/reference	1.24336	0.48
52DAP/reference	1.48355	0.044
57DAP/reference	3.6466	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.67168	0.916
26DAP/20DAP	1.14964	0.931
34DAP/26DAP	0.65719	0.084
51DAP/34DAP	1.61462	0.339
52DAP/51DAP	0.89212	1
53DAP/52DAP	1.14054	0.623
55DAP/53DAP	0.84812	0.159
57DAP/55DAP	0.78656	0.271
62DAP/57DAP	1.47338	0.185
68DAP/62DAP	14.0101	0.022
68DAP/14DAP	9.47535	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.37567	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.36342	0.059
Mature Green Tomato/Ripe Tomato	0.64873	0.031
Immature Eggplant/Mature Eggplant	1.0968	0.165
Ripe Pepper/Ripe Tomato	4.02044	0.256
Mature Eggplant/Ripe Tomato	1.41365	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13849	0.591
1-1-2/M82	1.33367
12-2/M82	0.87226
12-4/M82	1.02725	1
1-3/M82	1.85057
2-1-1/M82	N/A	N/A
2-1/M82	0.60446
2-6/M82	0.84461	1
3-2/M82	1.29608
4-1-1/M82	1.21453	0.966
4-1/M82	0.67154
4-3-2/M82	1.40177
4-3/M82	0.8765	0.611
5-3/M82	1.0206	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.90049
7-2/M82	1.14028	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.18436	0.365
IL2-6/WTpooled	1.00957	1
IL7-5/WTpooled	0.93049	1
IL7-3/WTpooled	0.96792	1
IL12-4/WTpooled	1.19753	0.532
IL1-4/WTpooled	0.99887	1
WT/WTpooled	0.92844	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	1.08106	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0299	0.894
DC3000/delta hrp 6h	1.10607	1
DC3000/delta hrp 12h	0.93894	1
DC3000/delta hrp 24h	0.83828	0.148

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	0.8868	1
Exp 36h	0.61746	0.406
Exp 60h	0.58195	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95774	1
Var 0h	0.72061	0.142
Var 12h I row2-row1	0.9686	1
Var 12h NI row2-row1	1.27148	0.161
Var 36h I row2-row1	1.11654	0.742
Var 36h NI row2-row1	0.59135	0.329
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.95252	1
Time course 0hI-0hNI	0.79669	0.069
Time course 12hI-12hNI	0.91561	0.431
Time course 36hI-36hNI	0.9391	0.426
Time course 60hI-60hNI	0.68879	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)	0.86888	0.246
transgenic ySAMdc/azygous control (breaker)	1.4312	0.248
transgenic ySAMdc/azygous control (red)	1.1569	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95551	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.54548	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.53666	0.087
Manapal/WT (break)	2.62861	0.183
Manapal/WT (red)	0.97757	0.863