Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.9.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.47477	0.03
27DAP/17DAP	0.54011	0.059
39DAP/27DAP	1.29727	0.759
41DAP/39DAP	0.85363	0.436
42DAP/41DAP	0.52566	0.262
43DAP/42DAP	1.11067	1
47DAP/43DAP	0.68777	0.17
52DAP/47DAP	0.91435	0.724
57DAP/52DAP	0.9554	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3043	0.081
17DAP/reference	0.94822	0.536
27DAP/reference	0.67344	0.023
39DAP/reference	0.60617	0.01
41DAP/reference	0.6608	0.008
42DAP/reference	0.62875	0.001
43DAP/reference	0.67997	0.018
47DAP/reference	0.61458	0.006
52DAP/reference	0.57904	0.024
57DAP/reference	0.71363	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95519	0.629
27DAP/17DAP	0.77995	0.169
39DAP/27DAP	0.76875	0.097
41DAP/39DAP	0.78164	0.096
42DAP/41DAP	1.07246	0.797
43DAP/42DAP	0.79324	0.042
47DAP/43DAP	0.78303	0.011
52DAP/47DAP	1.22138	0.512
57DAP/52DAP	1.05972	0.813
57DAP/7DAP	0.49985	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38303	0.6
17DAP/reference	0.96804	0.447
27DAP/reference	0.86133	0.062
39DAP/reference	1.07328	0.21
41DAP/reference	0.888	0.122
42DAP/reference	0.94765	0.248
43DAP/reference	0.89143	0.031
47DAP/reference	1.07615	0.525
52DAP/reference	1.05209	0.599
57DAP/reference	1.07563	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31655	0.201
17DAP/reference	1.01191	0.873
27DAP/reference	0.7971	0.024
39DAP/reference	0.53499	0.014
41DAP/reference	0.78126	0.07
42DAP/reference	0.80535	0.023
43DAP/reference	0.67209	0.007
47DAP/reference	0.66979	0.01
52DAP/reference	0.31205	0.031
57DAP/reference	0.43313	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07594	0.882
17DAP/reference	0.89602	0.322
27DAP/reference	0.73621	0.047
39DAP/reference	0.7975	0.083
41DAP/reference	0.84766	0.132
42DAP/reference	0.67252	0.032
43DAP/reference	0.81167	0.143
47DAP/reference	0.39424	0.005
52DAP/reference	0.74986	0.134
57DAP/reference	0.68612	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91031	1
26DAP/20DAP	2.40441	0.098
34DAP/26DAP	0.67241	0.107
51DAP/34DAP	0.69316	0.209
52DAP/51DAP	1.11657	0.925
53DAP/52DAP	1.28482	0.24
55DAP/53DAP	0.98255	0.886
57DAP/55DAP	0.97869	0.828
62DAP/57DAP	1.10325	0.723
68DAP/62DAP	1.33509	0.8
68DAP/14DAP	1.14584	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.71398	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.18796	0.058
Mature Green Tomato/Ripe Tomato	23.0183	0.015
Immature Eggplant/Mature Eggplant	0.37225	0.057
Ripe Pepper/Ripe Tomato	8.18518	0.256
Mature Eggplant/Ripe Tomato	38.2314	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99761
12-2/M82	N/A	N/A
12-4/M82	0.82814
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	0.97373
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07915
IL2-6/WTpooled	1.04912	0.584
IL7-5/WTpooled	0.41535
IL7-3/WTpooled	0.86991	0.418
IL12-4/WTpooled	0.89979	0.581
IL1-4/WTpooled	0.83845	0.699
WT/WTpooled	0.96565	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	0.74751	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98356	1
DC3000/delta hrp 6h	1.10562	0.857
DC3000/delta hrp 12h	1.36461	1
DC3000/delta hrp 24h	1.49973	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68426	0.03
DC3000 delta B/DC3000 delta AB	0.66464	0.048

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.62993	0.328
Exp 36h	0.5512	0.406
Exp 60h	0.44561	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05466	1
Var 0h	0.88841	0.933
Var 12h I row2-row1	0.67314	0.295
Var 12h NI row2-row1	1.02906	1
Var 36h I row2-row1	1.20464	1
Var 36h NI row2-row1	1.63608	1
Var 60h I row2-row1	0.90208	0.285
Var 60h NI row2-row1	1.00466	1
Time course 0hI-0hNI	0.94353	0.23
Time course 12hI-12hNI	0.86531	0.062
Time course 36hI-36hNI	0.59258	0.023
Time course 60hI-60hNI	0.17316	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)	0.92992	0.391
transgenic ySAMdc/azygous control (breaker)	1.07975	1
transgenic ySAMdc/azygous control (red)	1.0393	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28885	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60981	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.38772	0.172
Manapal/WT (break)	0.97829	1
Manapal/WT (red)	1.19365	1