Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.15.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9415	0.652
27DAP/17DAP	1.40837	0.581
39DAP/27DAP	3.28495	0.429
41DAP/39DAP	2.2212	0.584
42DAP/41DAP	1.03626	1
43DAP/42DAP	1.40048	1
47DAP/43DAP	0.24497	0.041
52DAP/47DAP	0.88781	0.666
57DAP/52DAP	0.75205	0.772

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89055	0.145
17DAP/reference	1.05667	0.492
27DAP/reference	1.00621	0.996
39DAP/reference	1.12333	0.098
41DAP/reference	1.12609	0.158
42DAP/reference	0.98866	0.469
43DAP/reference	0.9934	0.84
47DAP/reference	1.11474	0.11
52DAP/reference	0.88618	0.177
57DAP/reference	0.97231	0.479

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87731	0.211
27DAP/17DAP	0.89938	0.821
39DAP/27DAP	1.19532	0.615
41DAP/39DAP	1.14675	0.868
42DAP/41DAP	0.92994	0.56
43DAP/42DAP	1.02097	1
47DAP/43DAP	0.93822	0.677
52DAP/47DAP	1.08415	0.799
57DAP/52DAP	0.9162	0.473
57DAP/7DAP	1.08045	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87311	0.224
17DAP/reference	1.00986	0.754
27DAP/reference	0.98971	0.283
39DAP/reference	1.01385	0.705
41DAP/reference	1.06371	0.291
42DAP/reference	0.96998	0.371
43DAP/reference	1.03175	0.325
47DAP/reference	1.07609	0.582
52DAP/reference	1.10628	0.229
57DAP/reference	1.06756	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92169	0.353
17DAP/reference	0.91043	0.124
27DAP/reference	0.90223	0.195
39DAP/reference	0.86822	0.129
41DAP/reference	0.91071	0.124
42DAP/reference	0.89801	0.073
43DAP/reference	0.93789	0.344
47DAP/reference	0.95269	0.292
52DAP/reference	0.9331	0.203
57DAP/reference	0.88694	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95095	0.183
17DAP/reference	0.92777	0.407
27DAP/reference	0.95214	0.165
39DAP/reference	0.8956	0.015
41DAP/reference	0.98195	0.459
42DAP/reference	0.9652	0.552
43DAP/reference	0.99301	0.767
47DAP/reference	1.13408	0.026
52DAP/reference	1.00133	0.871
57DAP/reference	0.80732	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08327	0.966
26DAP/20DAP	0.84812	0.317
34DAP/26DAP	0.91095	0.898
51DAP/34DAP	1.29201	0.177
52DAP/51DAP	0.81779	1
53DAP/52DAP	1.81576	0.024
55DAP/53DAP	0.89123	0.35
57DAP/55DAP	1.03157	0.997
62DAP/57DAP	0.91134	0.681
68DAP/62DAP	1.38537	0.472
68DAP/14DAP	0.82868	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65457	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48528	0.094
Mature Green Tomato/Ripe Tomato	5.58469	0.016
Immature Eggplant/Mature Eggplant	0.49445	0.058
Ripe Pepper/Ripe Tomato	1.16243	1
Mature Eggplant/Ripe Tomato	0.39189	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15529	0.742
1-1-2/M82	1.16126	1
12-2/M82	1.05511	1
12-4/M82	1.0033	1
1-3/M82	1.25451	0.277
2-1-1/M82	1.12084	0.764
2-1/M82	0.63091	0.322
2-6/M82	1.25009	0.395
3-2/M82	2.15487	0.84
4-1-1/M82	1.53664	0.968
4-1/M82	0.79491
4-3-2/M82	2.96581	0.508
4-3/M82	1.76897	0.268
5-3/M82	0.80782	1
6-2/M82	1.38362	1
6-3/M82	0.92021	0.857
7-1/M82	0.84947	1
7-2/M82	1.05141	1
9-3-2/M82	2.86095	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.23017	1
IL12-4/WTpooled	1.6363	0.538
IL1-4/WTpooled	0.72803
WT/WTpooled	1.02874	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	1.57046	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90988	0.849
DC3000/delta hrp 6h	0.91587	0.95
DC3000/delta hrp 12h	0.9638	1
DC3000/delta hrp 24h	1.01516	0.797

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	0.77887	0.317

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.29725	0.254
Exp 36h	1.71564	0.409
Exp 60h	1.55849	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0555	1
Var 0h	1.05348	1
Var 12h I row2-row1	0.81175	0.514
Var 12h NI row2-row1	0.87765	0.713
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	0.88796
Var 60h I row2-row1	0.98932	1
Var 60h NI row2-row1	0.8797	0.932
Time course 0hI-0hNI	0.97767	0.934
Time course 12hI-12hNI	1.14794	0.201
Time course 36hI-36hNI	1.13862	0.166
Time course 60hI-60hNI	3.13816	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)	1.0242	0.384
transgenic ySAMdc/azygous control (breaker)	0.83183	0.142
transgenic ySAMdc/azygous control (red)	1.04361	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04907	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09773	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93407	1
Manapal/WT (break)	0.91603	0.333
Manapal/WT (red)	0.61854	0.199