Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97964	0.743
27DAP/17DAP	0.98972	0.978
39DAP/27DAP	0.75883	0.335
41DAP/39DAP	1.72562	0.663
42DAP/41DAP	0.99829	1
43DAP/42DAP	1.18743	0.785
47DAP/43DAP	1.39778	0.349
52DAP/47DAP	1.18018	0.819
57DAP/52DAP	1.0611	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22511	0.303
17DAP/reference	1.33813	0.035
27DAP/reference	1.25826	0.042
39DAP/reference	1.23418	0.076
41DAP/reference	1.46094	0.013
42DAP/reference	1.32179	0.012
43DAP/reference	1.16642	0.325
47DAP/reference	1.34487	0.142
52DAP/reference	1.52852	0.019
57DAP/reference	1.03383	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4153	0.039
27DAP/17DAP	0.94192	0.821
39DAP/27DAP	0.98622	0.908
41DAP/39DAP	1.14365	0.837
42DAP/41DAP	1.11501	0.514
43DAP/42DAP	0.93486	0.447
47DAP/43DAP	1.04185	0.772
52DAP/47DAP	1.0452	0.9
57DAP/52DAP	1.2667	0.293
57DAP/7DAP	0.97714	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1479	0.201
17DAP/reference	1.01399	1
27DAP/reference	0.998	0.748
39DAP/reference	0.97516	0.411
41DAP/reference	1.04849	0.767
42DAP/reference	1.14733	0.1
43DAP/reference	1.11443	0.188
47DAP/reference	1.17641	0.285
52DAP/reference	1.1908	0.011
57DAP/reference	1.18464	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30826	0.134
17DAP/reference	1.50758	0.053
27DAP/reference	1.52158	0.033
39DAP/reference	1.21277	0.136
41DAP/reference	1.61623	0.007
42DAP/reference	1.39151	0.01
43DAP/reference	1.24526	0.144
47DAP/reference	1.21146	0.035
52DAP/reference	1.16364	0.343
57DAP/reference	1.38159	0.155

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22206	0.056
17DAP/reference	1.08369	0.563
27DAP/reference	0.82049	0.034
39DAP/reference	1.11612	0.091
41DAP/reference	1.23052	0.15
42DAP/reference	1.41148	0.063
43DAP/reference	1.30114	0.02
47DAP/reference	1.09411	0.585
52DAP/reference	1.12671	0.558
57DAP/reference	1.68005	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15761	1
26DAP/20DAP	1.09683	0.826
34DAP/26DAP	1.10524	0.542
51DAP/34DAP	0.85974	0.305
52DAP/51DAP	1.04606	0.836
53DAP/52DAP	0.84882	0.265
55DAP/53DAP	1.21753	0.504
57DAP/55DAP	0.72048	0.123
62DAP/57DAP	0.9457	0.871
68DAP/62DAP	1.27159	0.95
68DAP/14DAP	0.86825	0.064

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84704	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.22037	0.058
Mature Green Tomato/Ripe Tomato	1.53418	0.028
Immature Eggplant/Mature Eggplant	0.64972	0.1
Ripe Pepper/Ripe Tomato	0.56861	0.224
Mature Eggplant/Ripe Tomato	1.09161	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.01319	1
12-2/M82	N/A	N/A
12-4/M82	0.93731	1
1-3/M82	1.19115	1
2-1-1/M82	1.17551
2-1/M82	1.13639
2-6/M82	N/A	N/A
3-2/M82	1.18755
4-1-1/M82	0.80993
4-1/M82	0.72073
4-3-2/M82	1.1888	0.241
4-3/M82	1.19116	1
5-3/M82	1.17663	1
6-2/M82	1.04002
6-3/M82	0.87112
7-1/M82	1.44741
7-2/M82	N/A	N/A
9-3-2/M82	0.82736	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.03165	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96195
IL12-4/WTpooled	1.04965	0.785
IL1-4/WTpooled	2.68284	1
WT/WTpooled	1.03733	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	1.20427	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93898	1
DC3000/delta hrp 6h	1.16133	1
DC3000/delta hrp 12h	1.26167	1
DC3000/delta hrp 24h	1.00156	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.58569	0.023
DC3000 delta B/DC3000 delta AB	0.50489	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14598	1
Exp 36h	0.81211	0.699
Exp 60h	0.74983	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01914	1
Var 0h	1.37273	0.421
Var 12h I row2-row1	0.71987	0.357
Var 12h NI row2-row1	0.89665	0.494
Var 36h I row2-row1	0.88915	0.805
Var 36h NI row2-row1	1.09955	1
Var 60h I row2-row1	1.28737	0.543
Var 60h NI row2-row1	1.05163	1
Time course 0hI-0hNI	1.08598	0.833
Time course 12hI-12hNI	1.00392	1
Time course 36hI-36hNI	0.8528	0.139
Time course 60hI-60hNI	0.17624	0.005

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)	0.96399	0.567
transgenic ySAMdc/azygous control (breaker)	0.92955	0.49
transgenic ySAMdc/azygous control (red)	0.842	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00135	0.673

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.2051	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.63679	0.084
Manapal/WT (break)	1.17181	0.381
Manapal/WT (red)	1.3316	0.222