Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75355	0.162
27DAP/17DAP	1.08545	1
39DAP/27DAP	2.15188	0.631
41DAP/39DAP	1.48073	0.584
42DAP/41DAP	1.13953	1
43DAP/42DAP	0.8913	0.765
47DAP/43DAP	1.144	0.909
52DAP/47DAP	1.98582	0.228
57DAP/52DAP	0.98615	0.978

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11589	0.303
17DAP/reference	0.91548	0.129
27DAP/reference	0.91983	0.208
39DAP/reference	0.96884	0.587
41DAP/reference	0.96536	0.542
42DAP/reference	0.93276	0.078
43DAP/reference	1.00618	1
47DAP/reference	1.05144	0.541
52DAP/reference	1.09103	0.548
57DAP/reference	0.96802	0.277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05061	1
27DAP/17DAP	0.74861	0.782
39DAP/27DAP	1.80577	0.441
41DAP/39DAP	1.09357	0.827
42DAP/41DAP	1.20824	0.651
43DAP/42DAP	0.9149	0.665
47DAP/43DAP	1.30175	0.618
52DAP/47DAP	1.01161	0.973
57DAP/52DAP	0.91825	0.601
57DAP/7DAP	0.66801	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27236	0.048
17DAP/reference	1.14802	0.269
27DAP/reference	1.15598	0.088
39DAP/reference	1.38876	0.02
41DAP/reference	1.3534	0.015
42DAP/reference	1.35392	0.059
43DAP/reference	1.1629	0.148
47DAP/reference	0.9904	0.671
52DAP/reference	1.24944	0.014
57DAP/reference	1.15364	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44878	0.052
17DAP/reference	0.99039	0.642
27DAP/reference	0.99025	0.619
39DAP/reference	0.99801	0.603
41DAP/reference	0.8262	0.021
42DAP/reference	0.95724	0.355
43DAP/reference	1.09736	0.655
47DAP/reference	1.04574	0.321
52DAP/reference	0.89262	0.037
57DAP/reference	1.26164	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27074	0.09
17DAP/reference	1.05137	0.627
27DAP/reference	1.16876	0.227
39DAP/reference	1.19749	0.022
41DAP/reference	1.28476	0.168
42DAP/reference	1.0112	1
43DAP/reference	1.31465	0.214
47DAP/reference	0.93629	0.348
52DAP/reference	1.12926	0.363
57DAP/reference	0.94801	0.387

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0352	1
26DAP/20DAP	0.75388
34DAP/26DAP	0.76531	0.148
51DAP/34DAP	1.03269	1
52DAP/51DAP	1.09599	0.742
53DAP/52DAP	0.93269	0.75
55DAP/53DAP	N/A	N/A
57DAP/55DAP	1.06351	0.915
62DAP/57DAP	1.01318	1
68DAP/62DAP	0.99756	0.914
68DAP/14DAP	1.32543	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99362	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.12696	0.018
Immature Eggplant/Mature Eggplant	5.31329	0.05
Ripe Pepper/Ripe Tomato	0.28419	0.293
Mature Eggplant/Ripe Tomato	0.27596	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.23322	1
1-1-2/M82	1.24818
12-2/M82	1.12191
12-4/M82	0.76271	0.33
1-3/M82	2.10178
2-1-1/M82	1.31209
2-1/M82	N/A	N/A
2-6/M82	1.24099	0.505
3-2/M82	0.67426	0.455
4-1-1/M82	2.64753	1
4-1/M82	0.97696
4-3-2/M82	1.55839
4-3/M82	1.59582	0.268
5-3/M82	1.07995	1
6-2/M82	0.73906
6-3/M82	1.00924
7-1/M82	N/A	N/A
7-2/M82	0.77027
9-3-2/M82	2.39344

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.10796	0.277
IL2-6/WTpooled	1.00955	1
IL7-5/WTpooled	0.91308	1
IL7-3/WTpooled	1.01247	1
IL12-4/WTpooled	0.67976	0.539
IL1-4/WTpooled	1.04998	1
WT/WTpooled	0.8994	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	1.19828	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06783	0.921
DC3000/delta hrp 6h	0.88423	0.95
DC3000/delta hrp 12h	0.98367	1
DC3000/delta hrp 24h	1.10941	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11153	0.29
DC3000 delta B/DC3000 delta AB	0.79277	0.129

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90634	1
Exp 36h	0.46368	0.404
Exp 60h	0.77522	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00308	1
Var 0h	0.76725	1
Var 12h I row2-row1	1.25782	0.544
Var 12h NI row2-row1	1.19119	0.34
Var 36h I row2-row1	1.41263	0.309
Var 36h NI row2-row1	0.86366	0.584
Var 60h I row2-row1	0.86167	0.832
Var 60h NI row2-row1	0.75879	0.335
Time course 0hI-0hNI	1.14117	0.218
Time course 12hI-12hNI	1.04345	0.82
Time course 36hI-36hNI	1.51476	0.012
Time course 60hI-60hNI	1.9283	0.009

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)	0.9758	0.229
transgenic ySAMdc/azygous control (breaker)	0.97093	1
transgenic ySAMdc/azygous control (red)	1.04041	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98032	0.136

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94975	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.59837	0.105
Manapal/WT (break)	1.06399	1
Manapal/WT (red)	N/A	N/A