Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.9.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96656	0.743
27DAP/17DAP	1.0656	0.905
39DAP/27DAP	0.86863	0.549
41DAP/39DAP	1.29154	0.451
42DAP/41DAP	1.05554	1
43DAP/42DAP	1.05438	1
47DAP/43DAP	0.92746	0.716
52DAP/47DAP	1.13591	0.811
57DAP/52DAP	1.10191	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98186	0.589
17DAP/reference	0.96961	0.448
27DAP/reference	0.94284	0.349
39DAP/reference	1.03407	0.359
41DAP/reference	1.02757	0.451
42DAP/reference	0.90702	0.004
43DAP/reference	1.0578	0.306
47DAP/reference	0.89579	0.06
52DAP/reference	0.80955	0.05
57DAP/reference	0.83147	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99121	0.826
27DAP/17DAP	0.99931	0.969
39DAP/27DAP	1.07064	0.626
41DAP/39DAP	1.02116	0.921
42DAP/41DAP	1.1558	0.46
43DAP/42DAP	1.04611	0.554
47DAP/43DAP	1.03345	0.939
52DAP/47DAP	0.95488	0.907
57DAP/52DAP	0.97866	0.753
57DAP/7DAP	1.53165	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90225	0.138
17DAP/reference	0.90283	0.031
27DAP/reference	0.8546	0.016
39DAP/reference	0.88434	0.011
41DAP/reference	0.87743	0.027
42DAP/reference	0.86017	0.029
43DAP/reference	0.87651	0.056
47DAP/reference	0.88923	0.293
52DAP/reference	0.85002	0.046
57DAP/reference	0.86852	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06131	0.491
17DAP/reference	1.04865	0.32
27DAP/reference	0.89597	0.203
39DAP/reference	0.89841	0.117
41DAP/reference	0.96476	0.212
42DAP/reference	0.78284	0.011
43DAP/reference	1.10345	0.479
47DAP/reference	0.90556	0.107
52DAP/reference	0.92878	0.203
57DAP/reference	1.14495	0.437

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90366	0.041
17DAP/reference	0.98961	0.763
27DAP/reference	0.82361	0.036
39DAP/reference	0.82116	0.009
41DAP/reference	0.82561	0.058
42DAP/reference	0.84104	0.22
43DAP/reference	0.78269	0.171
47DAP/reference	0.89804	0.296
52DAP/reference	0.88195	0.31
57DAP/reference	0.48854	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06026	0.966
26DAP/20DAP	1.08866	0.663
34DAP/26DAP	0.85657	0.214
51DAP/34DAP	1.22872	0.058
52DAP/51DAP	0.99189	1
53DAP/52DAP	0.91291
55DAP/53DAP	0.92119	0.686
57DAP/55DAP	1.08777	0.779
62DAP/57DAP	1.12173	0.515
68DAP/62DAP	1.07236	1
68DAP/14DAP	0.95147	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9692	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59122	0.127
Mature Green Tomato/Ripe Tomato	1.00654	0.835
Immature Eggplant/Mature Eggplant	1.12972	0.23
Ripe Pepper/Ripe Tomato	2.75038	1
Mature Eggplant/Ripe Tomato	1.32563	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92288	0.883
1-1-2/M82	0.90447	1
12-2/M82	1.1634	0.61
12-4/M82	0.9329	1
1-3/M82	0.89063	0.441
2-1-1/M82	1.47889	0.689
2-1/M82	1.13636	1
2-6/M82	1.01841	1
3-2/M82	1.02266	0.967
4-1-1/M82	0.92129	1
4-1/M82	0.94059	1
4-3-2/M82	0.82562	0.487
4-3/M82	0.79689	1
5-3/M82	1.05249	1
6-2/M82	0.93686	1
6-3/M82	0.91662	0.982
7-1/M82	0.67345
7-2/M82	1.13218	0.385
9-3-2/M82	0.87201	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00742	1
IL7-5/WTpooled	1.27818
IL7-3/WTpooled	0.88649	0.418
IL12-4/WTpooled	0.88772	0.71
IL1-4/WTpooled	1.03443	1
WT/WTpooled	0.96687	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	1.31494	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07167	0.758
DC3000/delta hrp 6h	0.96617	0.95
DC3000/delta hrp 12h	1.20705	1
DC3000/delta hrp 24h	1.1132	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.29423	0.121
DC3000 delta B/DC3000 delta AB	1.29745	0.128

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17548	1
Exp 36h	1.14099	1
Exp 60h	1.29596	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9926	1
Var 0h	1.22244	0.421
Var 12h I row2-row1	1.03257	0.736
Var 12h NI row2-row1	1.0595	1
Var 36h I row2-row1	0.9673	1
Var 36h NI row2-row1	0.89347	0.478
Var 60h I row2-row1	1.03388	1
Var 60h NI row2-row1	0.9174	0.756
Time course 0hI-0hNI	1.09407	0.662
Time course 12hI-12hNI	1.0238	0.77
Time course 36hI-36hNI	1.27129	0.007
Time course 60hI-60hNI	2.51996	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)	1.00734	0.612
transgenic ySAMdc/azygous control (breaker)	1.17652	1
transgenic ySAMdc/azygous control (red)	0.97514	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02646	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65504	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07666	0.307
Manapal/WT (break)	0.87922	1
Manapal/WT (red)	0.71746	0.183