Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.4.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.32931	0.014
27DAP/17DAP	0.77554	0.389
39DAP/27DAP	1.39545	0.225
41DAP/39DAP	0.65219	0.055
42DAP/41DAP	0.88594	1
43DAP/42DAP	1.42714	0.207
47DAP/43DAP	0.256	0.041
52DAP/47DAP	0.61284	0.148
57DAP/52DAP	1.1097	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34489	0.007
17DAP/reference	1.02845	0.427
27DAP/reference	1.01986	0.696
39DAP/reference	1.02252	0.747
41DAP/reference	0.99446	0.814
42DAP/reference	1.16526	0.001
43DAP/reference	0.95446	0.377
47DAP/reference	0.90752	0.007
52DAP/reference	0.95008	0.31
57DAP/reference	1.00331	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.30754	0.022
27DAP/17DAP	1.30789	0.075
39DAP/27DAP	1.01944	0.832
41DAP/39DAP	0.41055	0.015
42DAP/41DAP	1.3226	0.389
43DAP/42DAP	2.74799	0.013
47DAP/43DAP	0.52005	0.008
52DAP/47DAP	0.49709	0.041
57DAP/52DAP	0.89556	0.494
57DAP/7DAP	0.35124	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.85667	0.027
17DAP/reference	2.01304	0.007
27DAP/reference	0.91404	0.088
39DAP/reference	1.34871	0.008
41DAP/reference	0.97246	0.469
42DAP/reference	1.45569	0.132
43DAP/reference	0.83157	0.121
47DAP/reference	1.33928	0.173
52DAP/reference	0.40433	0.011
57DAP/reference	0.35189	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26722	0.55
17DAP/reference	1.30508	0.151
27DAP/reference	0.99024	0.598
39DAP/reference	1.08785	0.764
41DAP/reference	1.03749	0.96
42DAP/reference	1.06267	0.915
43DAP/reference	0.7971	0.06
47DAP/reference	1.03768	0.603
52DAP/reference	1.03751	0.528
57DAP/reference	0.81322	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73554	0.02
17DAP/reference	1.68849	0.326
27DAP/reference	1.54416	0.023
39DAP/reference	1.38743	0.043
41DAP/reference	0.90084	0.185
42DAP/reference	1.80518	0.009
43DAP/reference	1.48723	0.044
47DAP/reference	0.83083	0.008
52DAP/reference	0.61351	0.072
57DAP/reference	0.90922	0.333

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07713	0.966
26DAP/20DAP	1.46965	0.121
34DAP/26DAP	0.96674	0.945
51DAP/34DAP	0.88532	0.579
52DAP/51DAP	0.89374	1
53DAP/52DAP	0.7487	0.25
55DAP/53DAP	1.07193	0.989
57DAP/55DAP	1.0458	0.906
62DAP/57DAP	0.98242	0.871
68DAP/62DAP	0.97939	0.863
68DAP/14DAP	0.92561	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.62842	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.49656	0.058
Mature Green Tomato/Ripe Tomato	15.0072	0.015
Immature Eggplant/Mature Eggplant	0.96226	0.594
Ripe Pepper/Ripe Tomato	1.09016	1
Mature Eggplant/Ripe Tomato	1.42775	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03801	1
1-1-2/M82	1.25427	1
12-2/M82	1.0107	1
12-4/M82	0.86092	0.619
1-3/M82	1.53467	1
2-1-1/M82	0.51871	0.465
2-1/M82	1.33368
2-6/M82	1.02717	1
3-2/M82	0.8808	0.428
4-1-1/M82	0.75517	1
4-1/M82	1.28498
4-3-2/M82	0.95175	1
4-3/M82	1.24513	1
5-3/M82	1.35939	1
6-2/M82	1.66826
6-3/M82	N/A	N/A
7-1/M82	1.23856	0.598
7-2/M82	1.09839	1
9-3-2/M82	1.58719

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.80366	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09431	1
IL12-4/WTpooled	1.02668	1
IL1-4/WTpooled	0.90682
WT/WTpooled	0.98571	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	0.96798	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05645	0.921
DC3000/delta hrp 6h	0.93614	0.95
DC3000/delta hrp 12h	0.94422	1
DC3000/delta hrp 24h	0.73192	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1445	0.052
DC3000 delta B/DC3000 delta AB	1.95246	0.046

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84361	1
Exp 36h	1.19513	1
Exp 60h	1.33425	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.19167	0.318
transgenic ySAMdc/azygous control (breaker)	1.3741	0.178
transgenic ySAMdc/azygous control (red)	0.90058	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07813	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78475	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.33229	0.307
Manapal/WT (break)	1.28037	1
Manapal/WT (red)	0.76609	0.424