Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55899	0.019
27DAP/17DAP	0.5334	0.048
39DAP/27DAP	0.85569	0.573
41DAP/39DAP	0.75973	0.256
42DAP/41DAP	1.36868	0.871
43DAP/42DAP	1.72417	0.234
47DAP/43DAP	0.60418	0.115
52DAP/47DAP	0.61849	0.146
57DAP/52DAP	0.91429	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.63412	0.006
17DAP/reference	1.1892	0.08
27DAP/reference	1.4162	0.011
39DAP/reference	0.90806	0.306
41DAP/reference	0.78574	0.049
42DAP/reference	1.18816	0.08
43DAP/reference	0.97166	0.631
47DAP/reference	0.85542	0.007
52DAP/reference	0.83377	0.128
57DAP/reference	1.00481	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69625	0.044
27DAP/17DAP	1.3716	0.06
39DAP/27DAP	0.56177	0.062
41DAP/39DAP	0.49172	0.013
42DAP/41DAP	1.12752	0.8
43DAP/42DAP	1.49493	0.028
47DAP/43DAP	0.80295	0.022
52DAP/47DAP	0.67965	0.064
57DAP/52DAP	0.81272	0.125
57DAP/7DAP	0.19141	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.05389	0.024
17DAP/reference	1.56138	0.011
27DAP/reference	1.14352	0.131
39DAP/reference	0.93942	0.146
41DAP/reference	0.85471	0.073
42DAP/reference	0.98332	0.531
43DAP/reference	1.04661	0.386
47DAP/reference	0.84568	0.168
52DAP/reference	0.83448	0.077
57DAP/reference	0.90409	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37746	0.116
17DAP/reference	1.42148	0.01
27DAP/reference	1.23063	0.217
39DAP/reference	0.83205	0.019
41DAP/reference	0.80903	0.051
42DAP/reference	0.97313	0.482
43DAP/reference	0.68632	0.004
47DAP/reference	0.87633	0.061
52DAP/reference	0.73078	0.004
57DAP/reference	0.66146	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.98943	0.015
17DAP/reference	1.62337	0.109
27DAP/reference	1.76547	0.014
39DAP/reference	1.12305	0.264
41DAP/reference	0.94568	0.331
42DAP/reference	1.22245	0.373
43DAP/reference	1.14072	0.209
47DAP/reference	0.93309	0.224
52DAP/reference	0.90622	0.376
57DAP/reference	0.95662	0.346

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89889	1
26DAP/20DAP	1.37421	0.182
34DAP/26DAP	0.91487	0.675
51DAP/34DAP	1.36017	0.072
52DAP/51DAP	0.8287	1
53DAP/52DAP	0.88941	0.498
55DAP/53DAP	0.38117	0.016
57DAP/55DAP	0.59501	0.018
62DAP/57DAP	1.56241	0.029
68DAP/62DAP	0.90921	0.406
68DAP/14DAP	0.84811	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.12747	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.41062	0.058
Mature Green Tomato/Ripe Tomato	16.0192	0.018
Immature Eggplant/Mature Eggplant	0.31827	0.058
Ripe Pepper/Ripe Tomato	5.62957	0.258
Mature Eggplant/Ripe Tomato	9.67786	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.35863
1-1-2/M82	1.0185	1
12-2/M82	1.0201	1
12-4/M82	0.90636	1
1-3/M82	1.20343
2-1-1/M82	N/A	N/A
2-1/M82	0.49082	0.322
2-6/M82	1.96988	0.594
3-2/M82	0.9511
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.02373	1
5-3/M82	0.54033
6-2/M82	1.80283
6-3/M82	0.957
7-1/M82	0.73065
7-2/M82	1.34451	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02643	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97065	1
IL12-4/WTpooled	1.06939	0.891
IL1-4/WTpooled	1.04601
WT/WTpooled	1.02027	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	0.89193	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95694	1
DC3000/delta hrp 6h	0.93447	0.95
DC3000/delta hrp 12h	1.06266	1
DC3000/delta hrp 24h	0.34811	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.45492	0.023
DC3000 delta B/DC3000 delta AB	0.46174	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91768	1
Exp 36h	0.79256	0.449
Exp 60h	0.61529	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01553	1
Var 0h	1.38712	0.936
Var 12h I row2-row1	0.76384	0.338
Var 12h NI row2-row1	0.94204	0.403
Var 36h I row2-row1	0.87353	0.805
Var 36h NI row2-row1	1.23578	0.276
Var 60h I row2-row1	0.91397	0.832
Var 60h NI row2-row1	0.98955	1
Time course 0hI-0hNI	0.9792	0.908
Time course 12hI-12hNI	1.0459	0.724
Time course 36hI-36hNI	0.88458	0.047
Time course 60hI-60hNI	0.13471	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)	1.01331	0.921
transgenic ySAMdc/azygous control (breaker)	0.90352	0.49
transgenic ySAMdc/azygous control (red)	1.35505	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84444	0.078

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.04935	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.67124	0.088
Manapal/WT (break)	2.30664	0.183
Manapal/WT (red)	1.70057	0.15