Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.14.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.55696	0.443
27DAP/17DAP	2.00387	0.134
39DAP/27DAP	3.30088	0.533
41DAP/39DAP	2.18731	0.468
42DAP/41DAP	1.01642	1
43DAP/42DAP	1.41343	1
47DAP/43DAP	0.23658	0.04
52DAP/47DAP	0.82403	0.521
57DAP/52DAP	0.92909	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78703	0.08
17DAP/reference	0.84449	0.065
27DAP/reference	1.09143	0.446
39DAP/reference	0.82971	0.085
41DAP/reference	0.75162	0.031
42DAP/reference	3.56843	0.043
43DAP/reference	0.95322	0.429
47DAP/reference	0.95787	0.322
52DAP/reference	0.7171	0.084
57DAP/reference	1.03895	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93056	0.289
27DAP/17DAP	1.11243	0.686
39DAP/27DAP	5.2702	0.022
41DAP/39DAP	5.01383	0.005
42DAP/41DAP	0.58601	0.007
43DAP/42DAP	0.40666	0.022
47DAP/43DAP	1.12069	0.331
52DAP/47DAP	1.33482	0.883
57DAP/52DAP	0.52914	0.176
57DAP/7DAP	0.98505	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17034	0.732
17DAP/reference	2.05797	0.008
27DAP/reference	2.2505	0.088
39DAP/reference	3.12813	0.016
41DAP/reference	1.4799	0.023
42DAP/reference	2.51472	0.046
43DAP/reference	1.98505	0.024
47DAP/reference	2.14799	0.033
52DAP/reference	2.66406	0.008
57DAP/reference	2.87809	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74049	0.018
17DAP/reference	1.07179	0.496
27DAP/reference	1.13082	0.283
39DAP/reference	2.48211	0.03
41DAP/reference	1.50943	0.016
42DAP/reference	1.96191	0.018
43DAP/reference	2.66314	0.033
47DAP/reference	3.57269	0.014
52DAP/reference	1.46076	0.014
57DAP/reference	3.68728	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02732	0.653
17DAP/reference	1.30129	0.311
27DAP/reference	1.56829	0.014
39DAP/reference	2.00047	0.006
41DAP/reference	1.95038	0.009
42DAP/reference	1.16678	0.391
43DAP/reference	1.2502	0.205
47DAP/reference	0.76589	0.017
52DAP/reference	1.68706	0.051
57DAP/reference	1.02734	0.902

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05256	1
26DAP/20DAP	0.98491	1
34DAP/26DAP	0.99303	1
51DAP/34DAP	1.34488
52DAP/51DAP	2.3284	0.454
53DAP/52DAP	1.05847	0.895
55DAP/53DAP	1.20848	0.848
57DAP/55DAP	1.2422	0.826
62DAP/57DAP	0.82283	0.088
68DAP/62DAP	1.08819	1
68DAP/14DAP	1.149	0.069

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	10.2179	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27558	0.089
Mature Green Tomato/Ripe Tomato	11.8416	0.015
Immature Eggplant/Mature Eggplant	0.8849	0.176
Ripe Pepper/Ripe Tomato	0.59896	0.224
Mature Eggplant/Ripe Tomato	1.69621	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.75725	0.503
1-1-2/M82	1.32476	1
12-2/M82	1.27884	1
12-4/M82	1.2416	1
1-3/M82	2.17576	0.248
2-1-1/M82	0.72967	0.465
2-1/M82	2.95209	0.32
2-6/M82	1.25925	0.385
3-2/M82	3.96911
4-1-1/M82	3.7024	0.876
4-1/M82	1.48775	0.853
4-3-2/M82	4.76756	0.508
4-3/M82	0.91031	1
5-3/M82	1.57478	0.496
6-2/M82	10.0499	0.235
6-3/M82	1.09018	1
7-1/M82	N/A	N/A
7-2/M82	1.85489	0.263
9-3-2/M82	3.1469

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.78379
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8519
IL12-4/WTpooled	0.80401
IL1-4/WTpooled	1.10386
WT/WTpooled	0.91911	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	1.62726	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06745	0.823
DC3000/delta hrp 6h	0.88837	0.95
DC3000/delta hrp 12h	0.8658	1
DC3000/delta hrp 24h	2.24697	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.20688	0.042
DC3000 delta B/DC3000 delta AB	4.493	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.47353	1
Exp 36h	1.3848	0.693
Exp 60h	2.37841	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02986	1
Var 0h	0.71974	0.457
Var 12h I row2-row1	1.01399	1
Var 12h NI row2-row1	2.85462	0.203
Var 36h I row2-row1	1.21147	0.742
Var 36h NI row2-row1	0.49516	0.478
Var 60h I row2-row1	1.11334	0.562
Var 60h NI row2-row1	0.73459	0.818
Time course 0hI-0hNI	2.0629	0.63
Time course 12hI-12hNI	1.9716	0.475
Time course 36hI-36hNI	10.3652	0.004
Time course 60hI-60hNI	94.3476	0.008

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)	0.42336	0.249
transgenic ySAMdc/azygous control (breaker)	0.91368	0.49
transgenic ySAMdc/azygous control (red)	1.13632	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09495	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.31153	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89635	1
Manapal/WT (break)	0.46404	0.333
Manapal/WT (red)	0.71089	0.503