Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.1.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94506	0.671
27DAP/17DAP	0.77515	0.29
39DAP/27DAP	2.20499	0.034
41DAP/39DAP	0.56562	0.045
42DAP/41DAP	1.52987	0.841
43DAP/42DAP	0.94728	0.887
47DAP/43DAP	0.82793	0.487
52DAP/47DAP	0.90672	0.685
57DAP/52DAP	0.93618	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.93545	0.018
17DAP/reference	1.34104	0.185
27DAP/reference	1.01014	0.867
39DAP/reference	1.39811	0.256
41DAP/reference	1.37304	0.041
42DAP/reference	2.19399	0.001
43DAP/reference	1.4967	0.014
47DAP/reference	1.61528	0.002
52DAP/reference	0.85772	0.131
57DAP/reference	1.16061	0.084

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09035	0.365
27DAP/17DAP	1.0296	0.957
39DAP/27DAP	0.78207	0.068
41DAP/39DAP	1.56715	0.417
42DAP/41DAP	0.8751	0.181
43DAP/42DAP	0.81282	0.029
47DAP/43DAP	1.0278	0.956
52DAP/47DAP	0.73813	0.038
57DAP/52DAP	1.02562	1
57DAP/7DAP	0.70895	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.93627	0.025
17DAP/reference	1.9274	0.018
27DAP/reference	2.46356	0.006
39DAP/reference	2.23509	0.006
41DAP/reference	2.14373	0.01
42DAP/reference	2.93864	0.006
43DAP/reference	2.33157	0.007
47DAP/reference	2.17882	0.014
52DAP/reference	3.16284	0.007
57DAP/reference	2.304	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04847	0.811
17DAP/reference	1.43477	0.04
27DAP/reference	1.83671	0.087
39DAP/reference	1.99961	0.016
41DAP/reference	1.89859	0.005
42DAP/reference	2.1317	0.007
43DAP/reference	1.3214	0.466
47DAP/reference	1.94917	0.008
52DAP/reference	0.87667	0.302
57DAP/reference	0.89873	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6193	0.024
17DAP/reference	1.85282	0.306
27DAP/reference	2.06541	0.016
39DAP/reference	2.42561	0.006
41DAP/reference	2.2313	0.006
42DAP/reference	2.80159	0.006
43DAP/reference	3.50978	0.007
47DAP/reference	1.21314	0.218
52DAP/reference	1.77218	0.046
57DAP/reference	1.92155	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08511	0.966
26DAP/20DAP	1.14882	0.962
34DAP/26DAP	1.61236	0.819
51DAP/34DAP	0.82387	0.436
52DAP/51DAP	0.76334	1
53DAP/52DAP	0.93603	0.741
55DAP/53DAP	0.82496	0.049
57DAP/55DAP	1.13364	0.543
62DAP/57DAP	0.75623	0.088
68DAP/62DAP	0.73387	0.245
68DAP/14DAP	1.3193	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.86606	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0445	0.666
Mature Green Tomato/Ripe Tomato	2.19382	0.016
Immature Eggplant/Mature Eggplant	1.03675	0.58
Ripe Pepper/Ripe Tomato	1.25042	0.258
Mature Eggplant/Ripe Tomato	0.87868	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02555	1
1-1-2/M82	1.19586	1
12-2/M82	1.0113	1
12-4/M82	1.26882	1
1-3/M82	1.23087	0.479
2-1-1/M82	1.04118	0.26
2-1/M82	0.74779	0.345
2-6/M82	0.91749	0.501
3-2/M82	1.07407	0.967
4-1-1/M82	1.04321	1
4-1/M82	1.48039	0.512
4-3-2/M82	1.75522	0.284
4-3/M82	1.11813	1
5-3/M82	0.98048	1
6-2/M82	1.09343	1
6-3/M82	0.97756	1
7-1/M82	0.90873	0.803
7-2/M82	1.06808	1
9-3-2/M82	1.31739	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82009	1
IL2-6/WTpooled	1.1402	0.659
IL7-5/WTpooled	1.08057	0.75
IL7-3/WTpooled	0.84071	0.31
IL12-4/WTpooled	1.07863	1
IL1-4/WTpooled	0.97006	1
WT/WTpooled	1.13846	0.957

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	1.16047	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05375	0.921
DC3000/delta hrp 6h	0.84986	0.95
DC3000/delta hrp 12h	1.33156	1
DC3000/delta hrp 24h	0.97659	0.851

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07149	0.29
DC3000 delta B/DC3000 delta AB	1.08046	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99022	1
Exp 36h	1.10319	1
Exp 60h	0.94706	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99678	1
Var 0h	0.97247	1
Var 12h I row2-row1	1.06855	0.795
Var 12h NI row2-row1	1.04981	1
Var 36h I row2-row1	1.46608	0.742
Var 36h NI row2-row1	1.27629	1
Var 60h I row2-row1	0.9459	0.952
Var 60h NI row2-row1	0.70152	0.302
Time course 0hI-0hNI	0.90913	0.367
Time course 12hI-12hNI	1.02325	0.803
Time course 36hI-36hNI	1.1741	0.401
Time course 60hI-60hNI	1.32581	0.053

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)	1.03956	0.863
transgenic ySAMdc/azygous control (breaker)	0.91449	0.49
transgenic ySAMdc/azygous control (red)	1.1198	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18117	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92998	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10714	0.307
Manapal/WT (break)	1.08019	1
Manapal/WT (red)	1.13037	0.413