Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.6.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8787	0.496
27DAP/17DAP	1.28561	0.793
39DAP/27DAP	0.91616	0.608
41DAP/39DAP	0.90037	0.59
42DAP/41DAP	1.3645	0.899
43DAP/42DAP	0.82252	0.589
47DAP/43DAP	1.25728	0.502
52DAP/47DAP	0.86573	0.63
57DAP/52DAP	1.08418	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97117	0.344
17DAP/reference	1.03045	0.282
27DAP/reference	0.96967	0.286
39DAP/reference	0.99337	0.874
41DAP/reference	0.99431	0.814
42DAP/reference	0.96858	0.188
43DAP/reference	1.01436	0.787
47DAP/reference	1.03201	0.773
52DAP/reference	0.94177	0.125
57DAP/reference	0.99081	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13834	0.431
27DAP/17DAP	0.98083	0.919
39DAP/27DAP	1.06435	0.663
41DAP/39DAP	0.98785	0.997
42DAP/41DAP	1.03543	1
43DAP/42DAP	1.07111	0.23
47DAP/43DAP	1.00508	1
52DAP/47DAP	0.95648	0.839
57DAP/52DAP	1.25558	0.421
57DAP/7DAP	0.75241	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01719	1
17DAP/reference	0.91887	0.518
27DAP/reference	0.69685	0.303
39DAP/reference	1.17628	0.74
41DAP/reference	1.08963	0.577
42DAP/reference	0.8852	0.033
43DAP/reference	1.11887	0.672
47DAP/reference	0.93692	0.504
52DAP/reference	1.25799	0.043
57DAP/reference	1.12939	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98947	0.811
17DAP/reference	1.01681	0.69
27DAP/reference	1.10547	0.26
39DAP/reference	1.04641	0.746
41DAP/reference	0.97412	0.364
42DAP/reference	0.95675	0.098
43DAP/reference	0.99973	0.846
47DAP/reference	0.93489	0.077
52DAP/reference	1.05562	0.259
57DAP/reference	1.07393	0.119

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90945	0.197
17DAP/reference	1.09787	0.784
27DAP/reference	0.75694	0.05
39DAP/reference	1.04424	0.496
41DAP/reference	1.77923	0.1
42DAP/reference	1.27569	0.294
43DAP/reference	2.03579	0.035
47DAP/reference	1.01795	0.585
52DAP/reference	1.08989	0.575
57DAP/reference	1.03911	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03515	0.966
26DAP/20DAP	0.96465	1
34DAP/26DAP	0.95215	0.954
51DAP/34DAP	1.17741	0.936
52DAP/51DAP	1.20696	0.542
53DAP/52DAP	0.96265	0.824
55DAP/53DAP	1.18576	0.589
57DAP/55DAP	0.94534	0.804
62DAP/57DAP	0.97354	0.994
68DAP/62DAP	0.99827	0.914
68DAP/14DAP	0.95366	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88713	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14715	0.176
Mature Green Tomato/Ripe Tomato	0.8829	0.182
Immature Eggplant/Mature Eggplant	0.95095	0.72
Ripe Pepper/Ripe Tomato	1.11325	1
Mature Eggplant/Ripe Tomato	0.53357	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09146
1-1-2/M82	1.12624	1
12-2/M82	N/A	N/A
12-4/M82	0.9258	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.89377
3-2/M82	0.88747
4-1-1/M82	N/A	N/A
4-1/M82	1.05621
4-3-2/M82	N/A	N/A
4-3/M82	1.21199
5-3/M82	1.02197	1
6-2/M82	0.73249
6-3/M82	N/A	N/A
7-1/M82	1.53153
7-2/M82	N/A	N/A
9-3-2/M82	0.91189	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16409
IL2-6/WTpooled	0.95868	0.383
IL7-5/WTpooled	0.85669
IL7-3/WTpooled	1.22657	0.362
IL12-4/WTpooled	0.84947	0.71
IL1-4/WTpooled	1.03259
WT/WTpooled	0.83569	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	0.83655	0.197

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94586	1
DC3000/delta hrp 6h	1.00574	0.95
DC3000/delta hrp 12h	0.93441	1
DC3000/delta hrp 24h	1.15092	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.27759
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11911	1
Exp 36h	1.23964	0.371
Exp 60h	1.24471	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.14806	1
Var 0h	1.16822	0.98
Var 12h I row2-row1	0.90777	0.705
Var 12h NI row2-row1	0.94107	0.627
Var 36h I row2-row1	1.00068	1
Var 36h NI row2-row1	1.51687	1
Var 60h I row2-row1	1.05235	1
Var 60h NI row2-row1	0.76389	0.904
Time course 0hI-0hNI	0.96737	0.845
Time course 12hI-12hNI	0.99196	1
Time course 36hI-36hNI	0.91324	0.142
Time course 60hI-60hNI	0.97826	0.646

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)	1.01814	0.699
transgenic ySAMdc/azygous control (breaker)	0.82441	0.173
transgenic ySAMdc/azygous control (red)	0.9789	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96753	0.112

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6643	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94744	1
Manapal/WT (break)	1.22415	0.14
Manapal/WT (red)	1.07698	1