Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.5.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87897	0.389
27DAP/17DAP	0.95067	0.899
39DAP/27DAP	1.08462	1
41DAP/39DAP	1.08237	0.814
42DAP/41DAP	0.96613	1
43DAP/42DAP	0.94698	0.867
47DAP/43DAP	0.6828	0.185
52DAP/47DAP	1.35579	0.397
57DAP/52DAP	1.16816	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14171	0.71
17DAP/reference	0.80203	0.01
27DAP/reference	1.0161	0.847
39DAP/reference	0.86249	0.146
41DAP/reference	0.74188	0.026
42DAP/reference	1.15886	0.144
43DAP/reference	0.95731	0.538
47DAP/reference	1.05297	0.794
52DAP/reference	1.09931	0.205
57DAP/reference	1.14718	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21008	0.558
27DAP/17DAP	1.06143	0.859
39DAP/27DAP	0.70562	0.031
41DAP/39DAP	0.98128	0.973
42DAP/41DAP	0.96515	0.704
43DAP/42DAP	0.88185	0.04
47DAP/43DAP	0.87437	0.243
52DAP/47DAP	1.69422	0.123
57DAP/52DAP	1.66901	0.101
57DAP/7DAP	1.12609	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43729	0.042
17DAP/reference	1.23541	0.18
27DAP/reference	1.0239	1
39DAP/reference	1.27731	0.038
41DAP/reference	1.28264	0.069
42DAP/reference	1.40536	0.01
43DAP/reference	1.47644	0.008
47DAP/reference	1.37809	0.025
52DAP/reference	1.21117	0.043
57DAP/reference	1.49279	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04967	0.832
17DAP/reference	0.99372	0.711
27DAP/reference	1.00293	0.711
39DAP/reference	1.00812	1
41DAP/reference	1.19115	0.166
42DAP/reference	0.94497	0.189
43DAP/reference	0.83461	0.144
47DAP/reference	0.82619	0.014
52DAP/reference	0.98246	0.537
57DAP/reference	0.84382	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15801	0.086
17DAP/reference	0.89046	0.322
27DAP/reference	0.91351	0.257
39DAP/reference	1.09049	0.613
41DAP/reference	1.00326	1
42DAP/reference	1.02146	0.802
43DAP/reference	1.04416	0.768
47DAP/reference	0.90064	0.224
52DAP/reference	1.14499	0.272
57DAP/reference	1.30754	0.027

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.064	1
26DAP/20DAP	2.25133	0.615
34DAP/26DAP	2.09396	1
51DAP/34DAP	1.64068	0.978
52DAP/51DAP	2.0188	0.036
53DAP/52DAP	1.06729	0.895
55DAP/53DAP	1.06509	0.782
57DAP/55DAP	1.03325	0.623
62DAP/57DAP	1.33003
68DAP/62DAP	1.13829	0.405
68DAP/14DAP	3.25436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.60708	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.39961	0.078
Mature Green Tomato/Ripe Tomato	0.65345	0.132
Immature Eggplant/Mature Eggplant	0.90728	0.197
Ripe Pepper/Ripe Tomato	1.41419	1
Mature Eggplant/Ripe Tomato	0.70807	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97103
1-1-2/M82	1.14724	1
12-2/M82	1.06013
12-4/M82	0.97903	1
1-3/M82	2.15983	0.479
2-1-1/M82	N/A	N/A
2-1/M82	0.53324
2-6/M82	0.90461	1
3-2/M82	1.36361	0.463
4-1-1/M82	1.25824	1
4-1/M82	0.94878	1
4-3-2/M82	0.76313
4-3/M82	0.64835	0.611
5-3/M82	1.1185	1
6-2/M82	1.25132
6-3/M82	1.0407	1
7-1/M82	1.2031	0.598
7-2/M82	1.22023	1
9-3-2/M82	1.11199	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94788	0.247
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.9284
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.37242	1
WT/WTpooled	0.70095

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	1.53602	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97278	1
DC3000/delta hrp 6h	0.96647	0.95
DC3000/delta hrp 12h	1.11667	1
DC3000/delta hrp 24h	0.94877	0.692

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01296	0.648
DC3000 delta B/DC3000 delta AB	1.11557	0.457

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95842	1
Exp 36h	0.90991	0.539
Exp 60h	1.02561	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01787	1
Var 0h	1.18775	0.782
Var 12h I row2-row1	0.92483	0.353
Var 12h NI row2-row1	1.0746	1
Var 36h I row2-row1	0.98876	1
Var 36h NI row2-row1	1.21103	0.482
Var 60h I row2-row1	0.83383	0.306
Var 60h NI row2-row1	0.91205	1
Time course 0hI-0hNI	0.88104	0.162
Time course 12hI-12hNI	0.97418	0.858
Time course 36hI-36hNI	0.86449	0.215
Time course 60hI-60hNI	0.73091	0.011

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)	0.99622	0.931
transgenic ySAMdc/azygous control (breaker)	1.21874	0.166
transgenic ySAMdc/azygous control (red)	0.95339	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90415	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8326	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23916	0.14
Manapal/WT (break)	0.9498	1
Manapal/WT (red)	1.09466	0.413