Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76702	0.162
27DAP/17DAP	0.89309	0.833
39DAP/27DAP	0.87367	0.549
41DAP/39DAP	1.03591	0.854
42DAP/41DAP	0.92318	1
43DAP/42DAP	0.85024	0.705
47DAP/43DAP	1.40448	0.361
52DAP/47DAP	1.37457	0.613
57DAP/52DAP	1.08419	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11624	0.334
17DAP/reference	1.22636	0.143
27DAP/reference	1.048	0.721
39DAP/reference	1.2729	0.236
41DAP/reference	1.4814	0.012
42DAP/reference	1.10159	0.151
43DAP/reference	1.00776	0.942
47DAP/reference	0.95266	0.3
52DAP/reference	0.91667	0.237
57DAP/reference	0.82867	0.029

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90396	0.442
27DAP/17DAP	1.13453	0.794
39DAP/27DAP	0.97835	0.852
41DAP/39DAP	1.12108	0.682
42DAP/41DAP	0.82145	0.298
43DAP/42DAP	1.11368	0.25
47DAP/43DAP	1.03177	0.914
52DAP/47DAP	0.81105	0.265
57DAP/52DAP	1.21126	0.798
57DAP/7DAP	1.13224	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98172	0.682
17DAP/reference	0.96315	0.124
27DAP/reference	0.93728	0.076
39DAP/reference	0.98656	0.354
41DAP/reference	0.908	0.05
42DAP/reference	0.90415	0.011
43DAP/reference	0.97544	0.44
47DAP/reference	0.89806	0.101
52DAP/reference	0.92273	0.304
57DAP/reference	0.87442	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.261	0.056
17DAP/reference	1.41704	0.026
27DAP/reference	1.0764	0.535
39DAP/reference	1.15816	0.316
41DAP/reference	1.07823	0.525
42DAP/reference	1.06983	0.826
43DAP/reference	1.43395	0.033
47DAP/reference	1.15595	0.176
52DAP/reference	1.33714	0.223
57DAP/reference	1.69517	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05717	0.631
17DAP/reference	1.1737	0.153
27DAP/reference	1.016	0.805
39DAP/reference	1.07449	0.1
41DAP/reference	1.12477	0.383
42DAP/reference	1.03242	0.5
43DAP/reference	1.00847	0.767
47DAP/reference	0.95488	0.371
52DAP/reference	1.06838	0.592
57DAP/reference	0.77807	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.51863	0.966
26DAP/20DAP	1.31291	0.504
34DAP/26DAP	0.96961	0.972
51DAP/34DAP	0.91928	0.624
52DAP/51DAP	1.26974	0.225
53DAP/52DAP	0.84113	0.221
55DAP/53DAP	1.0494	0.925
57DAP/55DAP	1.02772	0.975
62DAP/57DAP	1.0091	1
68DAP/62DAP	0.63628	0.211
68DAP/14DAP	0.583	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94605	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.65595	0.411
Immature Eggplant/Mature Eggplant	1.15863	0.3
Ripe Pepper/Ripe Tomato	0.72399	1
Mature Eggplant/Ripe Tomato	1.6556	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31015
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.47528
1-3/M82	0.89287
2-1-1/M82	0.9218
2-1/M82	1.32787
2-6/M82	1.01679	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.33143
5-3/M82	0.91421	1
6-2/M82	N/A	N/A
6-3/M82	1.35927
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	2.23472	0.277
IL2-6/WTpooled	0.99253	1
IL7-5/WTpooled	1.78273	1
IL7-3/WTpooled	1.28419	1
IL12-4/WTpooled	1.08131	0.557
IL1-4/WTpooled	1.86544	1
WT/WTpooled	1.04482	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	1.03684	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99719	1
DC3000/delta hrp 6h	0.93939	0.95
DC3000/delta hrp 12h	1.08582	1
DC3000/delta hrp 24h	1.12576	0.37

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17878	0.042
DC3000 delta B/DC3000 delta AB	0.77293	0.337

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9478	1
Exp 36h	1.03483	1
Exp 60h	0.94817	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95831	1
Var 0h	0.89271	0.457
Var 12h I row2-row1	1.0873	0.506
Var 12h NI row2-row1	1.08427	1
Var 36h I row2-row1	0.72112	0.805
Var 36h NI row2-row1	0.76361	0.645
Var 60h I row2-row1	0.86092	0.285
Var 60h NI row2-row1	1.25338	0.904
Time course 0hI-0hNI	0.97705	0.911
Time course 12hI-12hNI	0.90667	0.618
Time course 36hI-36hNI	0.8656	0.084
Time course 60hI-60hNI	1.04346	0.673

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)	1.00342	1
transgenic ySAMdc/azygous control (breaker)	1.08186	1
transgenic ySAMdc/azygous control (red)	0.96244	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99102	0.588

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17792	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0549	1
Manapal/WT (break)	1.08786	0.183
Manapal/WT (red)	0.87453	0.184