Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92608	0.617
27DAP/17DAP	0.93217	0.879
39DAP/27DAP	1.0943	0.845
41DAP/39DAP	0.89248	0.566
42DAP/41DAP	1.08096	0.937
43DAP/42DAP	0.95741	0.895
47DAP/43DAP	1.03974	0.999
52DAP/47DAP	1.02447	0.957
57DAP/52DAP	1.15032	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91158	0.106
17DAP/reference	1.16418	0.045
27DAP/reference	0.95781	0.61
39DAP/reference	1.0164	0.828
41DAP/reference	1.18658	0.013
42DAP/reference	1.07937	0.299
43DAP/reference	1.16491	0.133
47DAP/reference	1.10377	0.295
52DAP/reference	0.99465	0.73
57DAP/reference	0.88639	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05499	0.372
27DAP/17DAP	1.06446	0.9
39DAP/27DAP	0.99399	1
41DAP/39DAP	0.94419	0.68
42DAP/41DAP	0.98737	0.83
43DAP/42DAP	0.90815	0.097
47DAP/43DAP	1.02094	0.892
52DAP/47DAP	1.05834	0.823
57DAP/52DAP	0.94008	0.448
57DAP/7DAP	1.08332	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09248	0.286
17DAP/reference	0.97322	0.389
27DAP/reference	1.12723	0.107
39DAP/reference	0.93838	0.264
41DAP/reference	1.08833	0.507
42DAP/reference	1.02474	0.889
43DAP/reference	1.30419	0.018
47DAP/reference	1.08593	0.337
52DAP/reference	0.9344	0.304
57DAP/reference	1.01171	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05712	0.507
17DAP/reference	1.18601	0.143
27DAP/reference	1.11192	0.235
39DAP/reference	1.08152	0.119
41DAP/reference	0.92359	0.231
42DAP/reference	1.05801	0.81
43DAP/reference	1.14089	0.288
47DAP/reference	1.0306	1
52DAP/reference	0.93451	0.037
57DAP/reference	1.22363	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98957	0.607
17DAP/reference	1.01093	0.934
27DAP/reference	1.15374	0.12
39DAP/reference	1.14267	0.365
41DAP/reference	1.17079	0.044
42DAP/reference	1.16511	0.214
43DAP/reference	1.11462	0.275
47DAP/reference	1.11978	0.015
52DAP/reference	1.08412	0.714
57DAP/reference	1.10814	0.539

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00809	1
26DAP/20DAP	1.11938	0.654
34DAP/26DAP	0.90318	0.412
51DAP/34DAP	1.1736	0.143
52DAP/51DAP	1.0068	1
53DAP/52DAP	1.01042	0.921
55DAP/53DAP	1.08085	0.764
57DAP/55DAP	1.01719	0.909
62DAP/57DAP	1.1299	0.029
68DAP/62DAP	0.85356	0.429
68DAP/14DAP	0.62011

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89229	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71094	0.193
Mature Green Tomato/Ripe Tomato	1.08323	0.69
Immature Eggplant/Mature Eggplant	1.46021	0.05
Ripe Pepper/Ripe Tomato	1.41882	0.256
Mature Eggplant/Ripe Tomato	0.90703	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13337	0.742
1-1-2/M82	0.98813	1
12-2/M82	N/A	N/A
12-4/M82	0.97754	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	1.14535
2-6/M82	N/A	N/A
3-2/M82	1.32049
4-1-1/M82	N/A	N/A
4-1/M82	1.35028
4-3-2/M82	N/A	N/A
4-3/M82	1.03328
5-3/M82	1.19131	0.415
6-2/M82	N/A	N/A
6-3/M82	0.79449
7-1/M82	1.01281
7-2/M82	1.03491	1
9-3-2/M82	1.1802

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77526	0.247
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.5953
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.71985	0.415
WT/WTpooled	N/A	N/A

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	0.84168	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99521	1
DC3000/delta hrp 6h	0.9688	0.95
DC3000/delta hrp 12h	0.92571	1
DC3000/delta hrp 24h	1.14836	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02035	1
DC3000 delta B/DC3000 delta AB	1.06484	0.539

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04887	1
Exp 36h	1.20697	1
Exp 60h	1.21373	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99841	1
Var 0h	0.70606	0.933
Var 12h I row2-row1	1.01494	1
Var 12h NI row2-row1	1.0703	1
Var 36h I row2-row1	1.06188	0.41
Var 36h NI row2-row1	1.11012	1
Var 60h I row2-row1	0.83951	0.374
Var 60h NI row2-row1	1.00192	1
Time course 0hI-0hNI	0.9761	0.911
Time course 12hI-12hNI	1.00566	1
Time course 36hI-36hNI	0.98595	0.621
Time course 60hI-60hNI	1.04776	0.359

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)	1.03121	0.748
transgenic ySAMdc/azygous control (breaker)	0.94368	0.49
transgenic ySAMdc/azygous control (red)	0.99286	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06625	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94243	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03647	1
Manapal/WT (break)	1.04326	1
Manapal/WT (red)	1.08217	0.413