Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98759	0.801
27DAP/17DAP	0.96587	0.964
39DAP/27DAP	1.7147	0.034
41DAP/39DAP	0.48049	0.041
42DAP/41DAP	1.28971	0.773
43DAP/42DAP	0.96803	0.895
47DAP/43DAP	0.82514	0.467
52DAP/47DAP	0.88076	0.626
57DAP/52DAP	1.37267	0.833

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03633	0.007
17DAP/reference	1.70563	0.036
27DAP/reference	1.20767	0.156
39DAP/reference	1.39829	0.249
41DAP/reference	1.38074	0.067
42DAP/reference	2.09809	0.001
43DAP/reference	1.38237	0.019
47DAP/reference	1.11552	0.048
52DAP/reference	0.90997	0.267
57DAP/reference	1.18314	0.094

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27225	0.148
27DAP/17DAP	0.87813	0.134
39DAP/27DAP	0.81864	0.073
41DAP/39DAP	1.15114	0.735
42DAP/41DAP	0.93996	0.545
43DAP/42DAP	0.82108	0.038
47DAP/43DAP	1.06386	0.618
52DAP/47DAP	0.84258	0.085
57DAP/52DAP	0.88036	0.348
57DAP/7DAP	0.84055	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75904	0.024
17DAP/reference	1.76283	0.006
27DAP/reference	2.31419	0.006
39DAP/reference	2.15379	0.005
41DAP/reference	1.96843	0.008
42DAP/reference	2.13463	0.007
43DAP/reference	1.62252	0.007
47DAP/reference	1.71078	0.014
52DAP/reference	2.32272	0.007
57DAP/reference	1.7651	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3822	0.234
17DAP/reference	1.98351	0.008
27DAP/reference	1.81291	0.097
39DAP/reference	2.06883	0.011
41DAP/reference	2.06338	0.005
42DAP/reference	2.29129	0.007
43DAP/reference	1.37819	0.617
47DAP/reference	2.14131	0.008
52DAP/reference	1.19078	0.017
57DAP/reference	1.22065	0.353

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56743	0.019
17DAP/reference	1.28872	0.217
27DAP/reference	1.58551	0.02
39DAP/reference	1.89736	0.004
41DAP/reference	1.88229	0.006
42DAP/reference	1.9555	0.006
43DAP/reference	1.80712	0.012
47DAP/reference	0.92695	0.357
52DAP/reference	1.61619	0.054
57DAP/reference	1.71446	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97041	1
26DAP/20DAP	1.60653	0.361
34DAP/26DAP	1.27981	1
51DAP/34DAP	0.99461	0.873
52DAP/51DAP	0.71902	0.151
53DAP/52DAP	0.72253	0.112
55DAP/53DAP	0.55048	0.037
57DAP/55DAP	0.71801	0.084
62DAP/57DAP	1.25139	0.185
68DAP/62DAP	0.92146	0.769
68DAP/14DAP	0.77359	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2109	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07458	0.176
Mature Green Tomato/Ripe Tomato	1.76326	0.086
Immature Eggplant/Mature Eggplant	0.93709	0.651
Ripe Pepper/Ripe Tomato	0.94082	1
Mature Eggplant/Ripe Tomato	2.38825	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.64182	0.402
1-1-2/M82	1.17302	1
12-2/M82	1.0571	1
12-4/M82	1.20153	1
1-3/M82	2.15029	0.277
2-1-1/M82	1.03862	1
2-1/M82	0.81865	0.519
2-6/M82	1.08466	0.594
3-2/M82	1.08786	0.463
4-1-1/M82	1.45725	0.876
4-1/M82	1.4266	1
4-3-2/M82	1.82474
4-3/M82	1.28149	1
5-3/M82	1.20254	1
6-2/M82	1.32757	0.253
6-3/M82	0.87199	0.659
7-1/M82	1.03477	0.598
7-2/M82	1.24047	0.385
9-3-2/M82	1.29071	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69873
IL2-6/WTpooled	0.83157	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04871	1
IL12-4/WTpooled	1.11404	0.785
IL1-4/WTpooled	0.92709	0.699
WT/WTpooled	0.9569	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	1.14942	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14702	0.914
DC3000/delta hrp 6h	1.00068	0.95
DC3000/delta hrp 12h	1.10825	1
DC3000/delta hrp 24h	0.94708	0.642

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15641
DC3000 delta B/DC3000 delta AB	0.97294	0.849

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98281	1
Exp 36h	1.27623	1
Exp 60h	0.95652	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98715	1
Var 0h	1.10792	0.936
Var 12h I row2-row1	0.90781	0.514
Var 12h NI row2-row1	1.28459	1
Var 36h I row2-row1	1.0017	1
Var 36h NI row2-row1	0.88735	0.645
Var 60h I row2-row1	1.0667	1
Var 60h NI row2-row1	0.77004	0.304
Time course 0hI-0hNI	0.89081	0.088
Time course 12hI-12hNI	1.05714	0.385
Time course 36hI-36hNI	1.27911	0.453
Time course 60hI-60hNI	1.27316	0.254

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)	0.97085	0.662
transgenic ySAMdc/azygous control (breaker)	1.00102	1
transgenic ySAMdc/azygous control (red)	1.123	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.40762	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75538	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71272	0.172
Manapal/WT (break)	1.0177	1
Manapal/WT (red)	1.37662	0.15