Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.9.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.692	0.03
27DAP/17DAP	1.0483	1
39DAP/27DAP	1.10691	0.873
41DAP/39DAP	0.94915	0.756
42DAP/41DAP	0.94075	1
43DAP/42DAP	0.9484	0.883
47DAP/43DAP	1.05029	0.965
52DAP/47DAP	0.88273	0.666
57DAP/52DAP	1.25773	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07255	0.587
17DAP/reference	0.76417	0.031
27DAP/reference	0.86933	0.137
39DAP/reference	0.8204	0.062
41DAP/reference	0.79793	0.031
42DAP/reference	0.88719	0.008
43DAP/reference	0.82581	0.026
47DAP/reference	0.80194	0.001
52DAP/reference	0.71096	0.024
57DAP/reference	0.71229	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62237	0.036
27DAP/17DAP	1.06555	0.905
39DAP/27DAP	0.83037	0.26
41DAP/39DAP	0.90461	0.446
42DAP/41DAP	1.03968	0.916
43DAP/42DAP	0.99934	1
47DAP/43DAP	0.93295	0.525
52DAP/47DAP	1.09239	0.713
57DAP/52DAP	1.05406	0.885
57DAP/7DAP	0.84737	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44687	0.032
17DAP/reference	1.24361	0.025
27DAP/reference	1.11653	0.026
39DAP/reference	0.7859	0.126
41DAP/reference	0.82761	0.067
42DAP/reference	1.00909	0.751
43DAP/reference	0.9224	0.183
47DAP/reference	0.8134	0.079
52DAP/reference	0.83865	0.066
57DAP/reference	0.80562	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14708	0.724
17DAP/reference	1.01854	0.805
27DAP/reference	0.91934	0.327
39DAP/reference	0.82746	0.132
41DAP/reference	0.99626	0.601
42DAP/reference	1.13863	0.115
43DAP/reference	0.8587	0.117
47DAP/reference	1.15159	0.138
52DAP/reference	0.6778	0.005
57DAP/reference	0.77381	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95227	0.016
17DAP/reference	1.53071	0.046
27DAP/reference	1.17041	0.033
39DAP/reference	0.96115	0.163
41DAP/reference	1.17076	0.222
42DAP/reference	0.87703	0.049
43DAP/reference	0.81946	0.024
47DAP/reference	0.77895	0.022
52DAP/reference	0.97543	0.573
57DAP/reference	0.91078	0.221

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8412	0.44
26DAP/20DAP	1.11492	0.931
34DAP/26DAP	1.3161	0.542
51DAP/34DAP	0.71976	0.077
52DAP/51DAP	0.87878	1
53DAP/52DAP	0.66872	0.049
55DAP/53DAP	0.83667	0.233
57DAP/55DAP	0.79362	0.286
62DAP/57DAP	0.96473	0.994
68DAP/62DAP	0.80218	0.345
68DAP/14DAP	0.80211	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66708	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.85327	0.058
Mature Green Tomato/Ripe Tomato	3.02219	0.015
Immature Eggplant/Mature Eggplant	0.5176	0.064
Ripe Pepper/Ripe Tomato	2.19549	0.258
Mature Eggplant/Ripe Tomato	4.66492	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19092	0.591
1-1-2/M82	1.02734	1
12-2/M82	N/A	N/A
12-4/M82	1.02259	1
1-3/M82	0.85979	0.501
2-1-1/M82	0.85181
2-1/M82	1.23438	1
2-6/M82	1.16287	0.452
3-2/M82	1.1893
4-1-1/M82	1.40367
4-1/M82	0.99028	1
4-3-2/M82	N/A	N/A
4-3/M82	1.1941	1
5-3/M82	1.15713	0.572
6-2/M82	1.24011
6-3/M82	0.96346	1
7-1/M82	0.92636
7-2/M82	1.01308	0.385
9-3-2/M82	0.93965

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94808	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.55292	1
IL12-4/WTpooled	1.16544	0.695
IL1-4/WTpooled	1.35589	1
WT/WTpooled	1.03633	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	0.80036	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03105	0.921
DC3000/delta hrp 6h	1.28746	1
DC3000/delta hrp 12h	1.14533	1
DC3000/delta hrp 24h	1.03139	0.346

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53871	0.023
DC3000 delta B/DC3000 delta AB	0.48631	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05758	1
Exp 36h	0.97819	0.943
Exp 60h	0.98226	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97461	1
Var 0h	1.42585	0.421
Var 12h I row2-row1	0.83358	0.514
Var 12h NI row2-row1	0.90091	0.394
Var 36h I row2-row1	1.15644	0.41
Var 36h NI row2-row1	1.27788	0.253
Var 60h I row2-row1	0.8114	0.832
Var 60h NI row2-row1	1.0659	0.904
Time course 0hI-0hNI	1.04518	0.852
Time course 12hI-12hNI	0.99639	1
Time course 36hI-36hNI	0.76202	0.028
Time course 60hI-60hNI	0.13591	0.005

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)	0.85347	0.309
transgenic ySAMdc/azygous control (breaker)	1.11065	0.248
transgenic ySAMdc/azygous control (red)	0.94131	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.77496	0.128

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.74865	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.42112	0.096
Manapal/WT (break)	1.83173	0.13
Manapal/WT (red)	1.93027	0.134