Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.15.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01036	0.919
27DAP/17DAP	1.1758	0.845
39DAP/27DAP	1.42539	0.244
41DAP/39DAP	1.25181	0.349
42DAP/41DAP	1.15876	0.933
43DAP/42DAP	0.81769	0.599
47DAP/43DAP	1.04708	0.828
52DAP/47DAP	1.6452	0.398
57DAP/52DAP	0.78939	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89385	0.118
17DAP/reference	0.93394	0.298
27DAP/reference	0.9836	0.741
39DAP/reference	1.01841	0.654
41DAP/reference	0.95874	0.154
42DAP/reference	0.94876	0.052
43DAP/reference	0.95091	0.273
47DAP/reference	0.91706	0.011
52DAP/reference	1.01501	1
57DAP/reference	1.07784	0.094

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95482	0.613
27DAP/17DAP	0.99398	0.943
39DAP/27DAP	1.05206	0.603
41DAP/39DAP	1.1666	0.682
42DAP/41DAP	0.94311	0.568
43DAP/42DAP	0.95203	0.383
47DAP/43DAP	1.01844	0.998
52DAP/47DAP	0.95644	0.834
57DAP/52DAP	0.93738	0.558
57DAP/7DAP	0.46247

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84021	0.082
17DAP/reference	0.8625	0.025
27DAP/reference	0.89754	0.023
39DAP/reference	0.90245	0.011
41DAP/reference	0.82292	0.013
42DAP/reference	0.90688	0.018
43DAP/reference	0.81092	0.011
47DAP/reference	1.03307	1
52DAP/reference	0.79392	0.03
57DAP/reference	0.79029	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9867	0.786
17DAP/reference	0.89109	0.083
27DAP/reference	0.93737	0.292
39DAP/reference	0.89627	0.087
41DAP/reference	0.92903	0.256
42DAP/reference	1.02186	1
43DAP/reference	1.1443	0.356
47DAP/reference	1.00557	0.77
52DAP/reference	0.96294	0.203
57DAP/reference	0.872	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94667	0.391
17DAP/reference	0.95423	0.426
27DAP/reference	0.85179	0.028
39DAP/reference	0.86888	0.037
41DAP/reference	0.94192	0.417
42DAP/reference	0.91112	0.134
43DAP/reference	0.82374	0.037
47DAP/reference	0.88919	0.161
52DAP/reference	0.81894	0.142
57DAP/reference	1.25109	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94458	1
26DAP/20DAP	0.84304	0.512
34DAP/26DAP	1.21707	0.819
51DAP/34DAP	0.88407	0.298
52DAP/51DAP	1.04623	0.842
53DAP/52DAP	1.01323	0.944
55DAP/53DAP	0.99262	0.886
57DAP/55DAP	0.92571	0.709
62DAP/57DAP	1.19347	0.35
68DAP/62DAP	0.89084	0.464
68DAP/14DAP	1.02886	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9372	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.43946	0.103
Mature Green Tomato/Ripe Tomato	0.84211	0.079
Immature Eggplant/Mature Eggplant	4.12399	0.05
Ripe Pepper/Ripe Tomato	3.26031	0.256
Mature Eggplant/Ripe Tomato	1.77895	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9911	1
1-1-2/M82	0.82326	0.958
12-2/M82	1.09954	1
12-4/M82	0.91267	1
1-3/M82	0.98942	1
2-1-1/M82	1.00747	1
2-1/M82	N/A	N/A
2-6/M82	1.0776	0.695
3-2/M82	0.83412
4-1-1/M82	1.19883	1
4-1/M82	1.04094
4-3-2/M82	N/A	N/A
4-3/M82	0.67434	1
5-3/M82	1.0301	1
6-2/M82	0.79628
6-3/M82	1.0029	1
7-1/M82	N/A	N/A
7-2/M82	1.09254	1
9-3-2/M82	0.82906	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.61183	0.243
IL2-6/WTpooled	0.91284	1
IL7-5/WTpooled	0.89159	0.559
IL7-3/WTpooled	0.65495	0.298
IL12-4/WTpooled	1.09708	1
IL1-4/WTpooled	0.90667	0.562
WT/WTpooled	1.08946	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	0.94501	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0408	0.921
DC3000/delta hrp 6h	1.0961	1
DC3000/delta hrp 12h	1.34568	1
DC3000/delta hrp 24h	0.95849	0.7

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.01394	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24153	1
Exp 36h	1.04647	1
Exp 60h	1.31222	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99025	1
Var 0h	0.86417	1
Var 12h I row2-row1	1.14134	0.296
Var 12h NI row2-row1	1.03846	1
Var 36h I row2-row1	0.80841	0.805
Var 36h NI row2-row1	0.95438	0.645
Var 60h I row2-row1	1.06483	0.543
Var 60h NI row2-row1	1.05112	1
Time course 0hI-0hNI	1.06017	0.799
Time course 12hI-12hNI	1.21707	0.023
Time course 36hI-36hNI	1.32793	0.019
Time course 60hI-60hNI	1.47579	0.008

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)	0.86724	0.234
transgenic ySAMdc/azygous control (breaker)	1.88169	0.178
transgenic ySAMdc/azygous control (red)	0.96162	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09799	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.49956	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.4084	1
Manapal/WT (break)	0.84351	1
Manapal/WT (red)	0.8677	0.36