Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	4.06582	0.029
27DAP/17DAP	2.68963	0.07
39DAP/27DAP	1.74754	0.146
41DAP/39DAP	0.64836	0.062
42DAP/41DAP	0.97516	1
43DAP/42DAP	1.22325	0.607
47DAP/43DAP	0.51541	0.049
52DAP/47DAP	0.82198	0.557
57DAP/52DAP	1.04799	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46371	0.025
17DAP/reference	1.31312	0.248
27DAP/reference	1.75075	0.011
39DAP/reference	2.26452	0.025
41DAP/reference	2.15341	0.013
42DAP/reference	1.712	0.001
43DAP/reference	1.38584	0.014
47DAP/reference	1.34843	0.021
52DAP/reference	0.87544	0.093
57DAP/reference	1.07983	0.724

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.83272	0.036
27DAP/17DAP	2.18014	0.027
39DAP/27DAP	1.04874	0.932
41DAP/39DAP	1.19811	1
42DAP/41DAP	1.12961	1
43DAP/42DAP	1.3501	0.176
47DAP/43DAP	0.82984	0.466
52DAP/47DAP	1.82296	0.317
57DAP/52DAP	0.96908	0.695
57DAP/7DAP	2.88466	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91313	0.296
17DAP/reference	1.44447	0.026
27DAP/reference	1.57002	0.026
39DAP/reference	2.55466	0.006
41DAP/reference	2.92921	0.008
42DAP/reference	2.18874	0.008
43DAP/reference	1.30135	0.048
47DAP/reference	1.25119	0.191
52DAP/reference	0.63986	0.011
57DAP/reference	0.6601	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5857	0.009
17DAP/reference	1.69845	0.019
27DAP/reference	2.38442	0.013
39DAP/reference	2.46301	0.011
41DAP/reference	1.66747	0.007
42DAP/reference	2.51304	0.007
43DAP/reference	1.48622	0.117
47DAP/reference	1.90593	0.008
52DAP/reference	2.83768	0.006
57DAP/reference	1.19769	0.314

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68774	0.032
17DAP/reference	0.85002	0.249
27DAP/reference	1.43395	0.015
39DAP/reference	1.59204	0.005
41DAP/reference	1.23974	0.168
42DAP/reference	1.3656	0.036
43DAP/reference	1.2992	0.06
47DAP/reference	1.24215	0.01
52DAP/reference	1.04781	0.851
57DAP/reference	0.72112	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14306	0.966
26DAP/20DAP	1.57567
34DAP/26DAP	0.92203	0.909
51DAP/34DAP	1.23877	0.483
52DAP/51DAP	0.42469	1
53DAP/52DAP	1.17121	0.819
55DAP/53DAP	1.03078	1
57DAP/55DAP	1.00172	0.944
62DAP/57DAP	1.12737	0.902
68DAP/62DAP	1.2075	0.523
68DAP/14DAP	1.40332	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	12.8169

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.38871	0.068
Mature Green Tomato/Ripe Tomato	1.79677	0.015
Immature Eggplant/Mature Eggplant	0.60872	0.066
Ripe Pepper/Ripe Tomato	0.09803	0.224
Mature Eggplant/Ripe Tomato	0.70044	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13916	0.551
1-1-2/M82	1.05648	1
12-2/M82	1.25479	1
12-4/M82	1.60297	1
1-3/M82	1.03422
2-1-1/M82	1.57305	0.366
2-1/M82	0.63448	0.74
2-6/M82	0.87173	1
3-2/M82	1.8378	0.84
4-1-1/M82	1.76222	1
4-1/M82	3.48915	0.853
4-3-2/M82	1.4475	0.241
4-3/M82	1.72069	0.268
5-3/M82	0.66672	0.642
6-2/M82	3.20423	0.235
6-3/M82	0.99254	1
7-1/M82	0.34053	0.509
7-2/M82	0.43098	0.57
9-3-2/M82	1.51861	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.38218	0.277
IL2-6/WTpooled	2.67715	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08052	1
IL12-4/WTpooled	0.86682	0.71
IL1-4/WTpooled	1.09323	1
WT/WTpooled	0.76828	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	1.08064	0.116

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00348	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.86726	1
DC3000/delta hrp 24h	1.03376	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.98956
DC3000 delta B/DC3000 delta AB	1.1627	0.437

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.15875	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02956	1
Var 0h	0.36255	0.142
Var 12h I row2-row1	0.88171	0.338
Var 12h NI row2-row1	1.08793	0.649
Var 36h I row2-row1	1.20735	0.309
Var 36h NI row2-row1	0.91473	0.549
Var 60h I row2-row1	0.81555	0.582
Var 60h NI row2-row1	0.83823	0.292
Time course 0hI-0hNI	1.12403	0.344
Time course 12hI-12hNI	0.93503	0.387
Time course 36hI-36hNI	1.06953	0.19
Time course 60hI-60hNI	1.64884	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)	1.05837	0.921
transgenic ySAMdc/azygous control (breaker)	1.07032	1
transgenic ySAMdc/azygous control (red)	1.09173	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08985	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87066	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98485	1
Manapal/WT (break)	0.89718	1
Manapal/WT (red)	1.68744	0.164