Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17202	0.512
27DAP/17DAP	0.72191	0.161
39DAP/27DAP	1.05956	1
41DAP/39DAP	0.80744	0.33
42DAP/41DAP	1.14096	0.929
43DAP/42DAP	1.40099	0.563
47DAP/43DAP	0.77905	0.321
52DAP/47DAP	0.6962	0.381
57DAP/52DAP	1.16523	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98895	0.661
17DAP/reference	0.80685	0.043
27DAP/reference	0.93002	0.385
39DAP/reference	0.98778	0.779
41DAP/reference	0.80738	0.065
42DAP/reference	1.01895	1
43DAP/reference	0.87792	0.107
47DAP/reference	0.86338	0.038
52DAP/reference	1.01318	0.709
57DAP/reference	1.1923	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07679	0.422
27DAP/17DAP	0.90866	0.475
39DAP/27DAP	0.65395	0.044
41DAP/39DAP	1.03941	1
42DAP/41DAP	1.01514	1
43DAP/42DAP	0.80857	0.034
47DAP/43DAP	0.77319	0.026
52DAP/47DAP	0.90365	0.575
57DAP/52DAP	0.61386	0.169
57DAP/7DAP	0.44584	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95359	0.027
17DAP/reference	1.42547	0.042
27DAP/reference	0.96723	0.462
39DAP/reference	1.00995	1
41DAP/reference	0.88308	0.146
42DAP/reference	1.01132	1
43DAP/reference	1.03215	0.873
47DAP/reference	1.30327	0.149
52DAP/reference	1.21101	0.105
57DAP/reference	1.06104	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03743	0.741
17DAP/reference	1.01374	0.898
27DAP/reference	1.06042	0.692
39DAP/reference	1.17249	0.146
41DAP/reference	0.93672	0.256
42DAP/reference	1.23801	0.038
43DAP/reference	1.42005	0.38
47DAP/reference	1.21682	0.037
52DAP/reference	1.0663	0.747
57DAP/reference	1.35262	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.13276	0.019
17DAP/reference	1.27134	0.321
27DAP/reference	1.02495	1
39DAP/reference	1.16813	0.057
41DAP/reference	1.11838	0.249
42DAP/reference	0.87848	0.134
43DAP/reference	0.93897	0.365
47DAP/reference	0.80017	0.022
52DAP/reference	0.69398	0.06
57DAP/reference	1.10794	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89416	1
26DAP/20DAP	1.07767	1
34DAP/26DAP	1.03833	1
51DAP/34DAP	0.67733	0.075
52DAP/51DAP	0.92288	1
53DAP/52DAP	0.79975	0.21
55DAP/53DAP	0.75459	0.037
57DAP/55DAP	0.81722	0.344
62DAP/57DAP	1.93279
68DAP/62DAP	1.19703	0.707
68DAP/14DAP	0.88802	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.59647	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.73822	0.058
Mature Green Tomato/Ripe Tomato	13.3261	0.015
Immature Eggplant/Mature Eggplant	0.50847	0.062
Ripe Pepper/Ripe Tomato	3.82172	0.258
Mature Eggplant/Ripe Tomato	3.04132	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.82037
12-2/M82	0.39069
12-4/M82	1.0198	1
1-3/M82	1.27705
2-1-1/M82	1.57398
2-1/M82	0.616
2-6/M82	1.36831
3-2/M82	1.49051
4-1-1/M82	N/A	N/A
4-1/M82	0.76385
4-3-2/M82	N/A	N/A
4-3/M82	1.42455	0.268
5-3/M82	1.15644	0.572
6-2/M82	1.9587	1
6-3/M82	N/A	N/A
7-1/M82	0.95918	0.398
7-2/M82	1.65847	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91617	0.321
IL2-6/WTpooled	1.04978	0.419
IL7-5/WTpooled	1.16875	0.792
IL7-3/WTpooled	0.92876	0.418
IL12-4/WTpooled	0.99823	1
IL1-4/WTpooled	1.13085	1
WT/WTpooled	0.95199	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	1.00564	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97184	1
DC3000/delta hrp 6h	1.12156	1
DC3000/delta hrp 12h	1.1147	1
DC3000/delta hrp 24h	0.61476	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54946	0.024
DC3000 delta B/DC3000 delta AB	0.49143	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23695	1
Exp 36h	1.12918	1
Exp 60h	1.59607	0.206

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96583	1
Var 0h	0.64135	1
Var 12h I row2-row1	0.69159	0.338
Var 12h NI row2-row1	0.87057	0.494
Var 36h I row2-row1	0.93381	0.805
Var 36h NI row2-row1	1.15227	0.482
Var 60h I row2-row1	1.09787	1
Var 60h NI row2-row1	1.06479	0.904
Time course 0hI-0hNI	0.95721	0.711
Time course 12hI-12hNI	1.00743	0.888
Time course 36hI-36hNI	0.78936	0.023
Time course 60hI-60hNI	0.11133	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)	0.77048	0.289
transgenic ySAMdc/azygous control (breaker)	12.9926	0.178
transgenic ySAMdc/azygous control (red)	1.39264	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99954	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19604	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.69432	0.083
Manapal/WT (break)	3.31078	0.183
Manapal/WT (red)	1.82478	0.126