Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.8.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92424	0.61
27DAP/17DAP	1.05658	0.883
39DAP/27DAP	1.68825	0.149
41DAP/39DAP	1.14176	0.54
42DAP/41DAP	2.43247	0.02
43DAP/42DAP	0.97325	0.925
47DAP/43DAP	0.92588	0.729
52DAP/47DAP	0.55253	0.072
57DAP/52DAP	0.98279	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78842	0.029
17DAP/reference	0.74834	0.016
27DAP/reference	0.88076	0.265
39DAP/reference	0.99699	0.957
41DAP/reference	0.79493	0.021
42DAP/reference	0.86906	0.026
43DAP/reference	1.02834	1
47DAP/reference	0.94636	0.258
52DAP/reference	1.21075	0.302
57DAP/reference	1.18304	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03126	0.99
27DAP/17DAP	1.39459	0.488
39DAP/27DAP	1.52357	0.043
41DAP/39DAP	0.64857	0.026
42DAP/41DAP	1.63552	0.005
43DAP/42DAP	3.06822	0.014
47DAP/43DAP	0.94953	0.712
52DAP/47DAP	1.20554	0.552
57DAP/52DAP	0.81272	0.356
57DAP/7DAP	1.83633	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8976	0.203
17DAP/reference	1.06858	0.688
27DAP/reference	1.13644	0.371
39DAP/reference	0.92751	0.411
41DAP/reference	0.93381	0.326
42DAP/reference	0.93013	0.304
43DAP/reference	0.94107	0.334
47DAP/reference	1.04511	0.504
52DAP/reference	0.86815	0.126
57DAP/reference	0.89943	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93429	0.426
17DAP/reference	0.84652	0.011
27DAP/reference	0.84535	0.027
39DAP/reference	0.86541	0.136
41DAP/reference	1.06028	0.629
42DAP/reference	0.91299	0.108
43DAP/reference	0.95479	0.478
47DAP/reference	0.87708	0.087
52DAP/reference	0.93826	0.302
57DAP/reference	0.84104	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02323	0.75
17DAP/reference	0.99526	0.825
27DAP/reference	1.76779	0.051
39DAP/reference	0.93765	0.271
41DAP/reference	0.93776	0.371
42DAP/reference	0.88779	0.22
43DAP/reference	1.03122	1
47DAP/reference	0.87773	0.278
52DAP/reference	0.80864	0.208
57DAP/reference	1.07848	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.47259	0.817
26DAP/20DAP	1.1237	0.953
34DAP/26DAP	1.86951	0.542
51DAP/34DAP	1.33525	0.303
52DAP/51DAP	1.1268	0.481
53DAP/52DAP	1.01425	0.944
55DAP/53DAP	0.98651	0.876
57DAP/55DAP	0.85101	0.479
62DAP/57DAP	0.93587	0.871
68DAP/62DAP	1.02887	0.977
68DAP/14DAP	1.22098	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.87206	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.77388	0.038
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.41644

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0094
1-1-2/M82	1.176	1
12-2/M82	N/A	N/A
12-4/M82	1.47119	1
1-3/M82	N/A	N/A
2-1-1/M82	0.85854
2-1/M82	N/A	N/A
2-6/M82	0.94164
3-2/M82	0.63047
4-1-1/M82	N/A	N/A
4-1/M82	2.65977
4-3-2/M82	1.34736	0.508
4-3/M82	1.47111	0.268
5-3/M82	1.29499	0.467
6-2/M82	N/A	N/A
6-3/M82	1.49692	1
7-1/M82	0.64323
7-2/M82	N/A	N/A
9-3-2/M82	1.5457	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.14799
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.25092
IL1-4/WTpooled	0.96631	1
WT/WTpooled	0.71555

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	1.07961	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07395	1
DC3000/delta hrp 6h	0.93085	0.95
DC3000/delta hrp 12h	1.00524	1
DC3000/delta hrp 24h	0.83406	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88531
DC3000 delta B/DC3000 delta AB	0.91175	0.483

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12926	1
Exp 36h	0.80259	0.449
Exp 60h	0.98684	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.12701
Var 0h	1.00918	1
Var 12h I row2-row1	0.96913	0.77
Var 12h NI row2-row1	0.91022	0.713
Var 36h I row2-row1	1.07805	0.742
Var 36h NI row2-row1	1.03129	1
Var 60h I row2-row1	0.86245	0.285
Var 60h NI row2-row1	1.02922	0.904
Time course 0hI-0hNI	1.07717	0.799
Time course 12hI-12hNI	1.06434	0.734
Time course 36hI-36hNI	1.13783	0.355
Time course 60hI-60hNI	1.81964	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)	0.89754	0.567
transgenic ySAMdc/azygous control (breaker)	1.03951	1
transgenic ySAMdc/azygous control (red)	0.93327	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95017	0.156

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.20376	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.54874	0.172
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.90667	0.607