Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.14.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04246	0.927
27DAP/17DAP	0.9421	0.913
39DAP/27DAP	0.95593	0.67
41DAP/39DAP	1.42285	0.292
42DAP/41DAP	0.80444	0.774
43DAP/42DAP	0.82979	0.495
47DAP/43DAP	0.87148	0.565
52DAP/47DAP	1.2444	0.898
57DAP/52DAP	0.74857	0.67

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9596	0.277
17DAP/reference	1.08314	0.154
27DAP/reference	0.92857	0.417
39DAP/reference	1.09001	0.191
41DAP/reference	1.08019	0.187
42DAP/reference	0.90075	0.021
43DAP/reference	0.99843	0.882
47DAP/reference	0.93263	0.242
52DAP/reference	0.84966	0.021
57DAP/reference	0.85201	0.086

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70775	0.033
27DAP/17DAP	1.23502	0.174
39DAP/27DAP	0.86293	0.291
41DAP/39DAP	0.93869	0.764
42DAP/41DAP	1.00777	1
43DAP/42DAP	1.15001	0.297
47DAP/43DAP	1.08019	0.812
52DAP/47DAP	0.98547	0.925
57DAP/52DAP	1.11244	0.497
57DAP/7DAP	0.99823	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86473	0.138
17DAP/reference	0.8198	0.082
27DAP/reference	0.93674	0.325
39DAP/reference	1.02119	0.779
41DAP/reference	0.88832	0.184
42DAP/reference	0.92229	0.151
43DAP/reference	0.78032	0.012
47DAP/reference	0.86918	0.066
52DAP/reference	0.79931	0.04
57DAP/reference	0.87864	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09675	0.626
17DAP/reference	1.12318	0.12
27DAP/reference	0.96265	0.483
39DAP/reference	0.97643	0.509
41DAP/reference	1.04973	0.893
42DAP/reference	1.02027	1
43DAP/reference	1.50547	0.03
47DAP/reference	1.07025	0.24
52DAP/reference	1.09586	0.528
57DAP/reference	1.18674	0.161

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83846	0.049
17DAP/reference	1.12836	0.518
27DAP/reference	0.92953	0.319
39DAP/reference	0.88036	0.022
41DAP/reference	0.95494	0.459
42DAP/reference	0.92474	0.361
43DAP/reference	0.82541	0.11
47DAP/reference	1.05381	0.519
52DAP/reference	0.79814	0.128
57DAP/reference	0.80291	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00586	1
26DAP/20DAP	1.20579	0.369
34DAP/26DAP	1.03509	1
51DAP/34DAP	0.92254	0.449
52DAP/51DAP	1.09283	0.171
53DAP/52DAP	1.02241	1
55DAP/53DAP	1.19	0.335
57DAP/55DAP	1.1911	0.969
62DAP/57DAP	1.00364	0.994
68DAP/62DAP	1.00566	0.863
68DAP/14DAP	0.69662	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11361	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.00609	0.774
Immature Eggplant/Mature Eggplant	1.45674
Ripe Pepper/Ripe Tomato	0.40664	0.293
Mature Eggplant/Ripe Tomato	0.54941	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08272	0.742
1-1-2/M82	0.58008
12-2/M82	1.39293	1
12-4/M82	0.80653
1-3/M82	0.89055	0.378
2-1-1/M82	1.03573	1
2-1/M82	0.86071	0.345
2-6/M82	1.01172	1
3-2/M82	0.91494
4-1-1/M82	0.87215	1
4-1/M82	0.61738	0.69
4-3-2/M82	1.0926	0.241
4-3/M82	1.35568	1
5-3/M82	0.95374	1
6-2/M82	0.76602
6-3/M82	1.08028	1
7-1/M82	N/A	N/A
7-2/M82	0.98566	1
9-3-2/M82	0.73378	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14335	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.98565	1
IL7-3/WTpooled	0.96114	1
IL12-4/WTpooled	1.21451	0.624
IL1-4/WTpooled	1.01043	1
WT/WTpooled	1.03446	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	0.93249	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13848	0.724
DC3000/delta hrp 6h	0.88388	0.95
DC3000/delta hrp 12h	0.90545	1
DC3000/delta hrp 24h	0.99741	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01868
DC3000 delta B/DC3000 delta AB	1.11473	0.528

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	1.19043	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01891	1
Var 0h	1.15747	0.782
Var 12h I row2-row1	1.19173	0.283
Var 12h NI row2-row1	0.88279	0.627
Var 36h I row2-row1	0.79303	0.805
Var 36h NI row2-row1	0.92889	0.645
Var 60h I row2-row1	1.06764	0.271
Var 60h NI row2-row1	1.01031	1
Time course 0hI-0hNI	1.03487	0.662
Time course 12hI-12hNI	1.01428	0.827
Time course 36hI-36hNI	0.90688	0.169
Time course 60hI-60hNI	0.94004	0.319

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)	1.10132	0.297
transgenic ySAMdc/azygous control (breaker)	0.84163	0.134
transgenic ySAMdc/azygous control (red)	1.0108	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96073	0.107

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30666	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03376	1
Manapal/WT (break)	0.77582	0.333
Manapal/WT (red)	0.8416	0.181