Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.10.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94375	0.543
27DAP/17DAP	1.04049	0.89
39DAP/27DAP	0.88626	0.474
41DAP/39DAP	1.30929	0.701
42DAP/41DAP	1.01455	1
43DAP/42DAP	0.9684	0.912
47DAP/43DAP	0.93552	0.768
52DAP/47DAP	1.10403	0.763
57DAP/52DAP	1.08115	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98638	0.601
17DAP/reference	0.98543	0.597
27DAP/reference	0.98412	0.61
39DAP/reference	1.02845	0.445
41DAP/reference	0.93613	0.341
42DAP/reference	0.93602	0.013
43DAP/reference	1.01947	0.596
47DAP/reference	0.99116	0.568
52DAP/reference	1.10121	0.072
57DAP/reference	0.99803	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96752	0.613
27DAP/17DAP	0.95218	0.179
39DAP/27DAP	1.21737	0.27
41DAP/39DAP	1.03577	0.727
42DAP/41DAP	1.0612	0.354
43DAP/42DAP	0.99879	1
47DAP/43DAP	1.00594	0.963
52DAP/47DAP	0.96332	0.814
57DAP/52DAP	0.95294	0.545
57DAP/7DAP	1.0276	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8224	0.071
17DAP/reference	0.50298	0.021
27DAP/reference	0.42243	0.01
39DAP/reference	0.33678	0.011
41DAP/reference	1.10929	0.619
42DAP/reference	0.43629	0.01
43DAP/reference	0.31586	0.009
47DAP/reference	0.62855	0.128
52DAP/reference	0.2861	0.009
57DAP/reference	0.27683	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09889	0.605
17DAP/reference	1.00096	0.873
27DAP/reference	0.95876	0.366
39DAP/reference	0.9684	0.37
41DAP/reference	0.98398	0.403
42DAP/reference	0.90176	0.016
43DAP/reference	0.78939	0.114
47DAP/reference	0.96529	0.277
52DAP/reference	0.98444	0.351
57DAP/reference	0.95226	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.08678	0.043
17DAP/reference	1.18228	0.496
27DAP/reference	0.50894	0.03
39DAP/reference	0.59582	0.018
41DAP/reference	0.51163	0.028
42DAP/reference	0.50301	0.025
43DAP/reference	0.57167	0.039
47DAP/reference	0.95841	0.325
52DAP/reference	0.6167	0.119
57DAP/reference	0.79	0.082

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99433	1
26DAP/20DAP	1.14389	0.464
34DAP/26DAP	1.01536	1
51DAP/34DAP	1.13771	0.215
52DAP/51DAP	0.99695	1
53DAP/52DAP	1.02318	0.858
55DAP/53DAP	0.95673	0.5
57DAP/55DAP	1.05059	0.854
62DAP/57DAP	0.97197	0.994
68DAP/62DAP	1.04574	0.858
68DAP/14DAP	1.07443	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00011	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.5219	0.058
Mature Green Tomato/Ripe Tomato	1.17546	0.267
Immature Eggplant/Mature Eggplant	0.64722	0.064
Ripe Pepper/Ripe Tomato	0.39582	0.293
Mature Eggplant/Ripe Tomato	2.14201	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08065	1
1-1-2/M82	0.9444	1
12-2/M82	1.0359	1
12-4/M82	0.91209	1
1-3/M82	0.89878	0.501
2-1-1/M82	1.16176	0.689
2-1/M82	1.16403	1
2-6/M82	0.95758	1
3-2/M82	0.96864	1
4-1-1/M82	0.97518	1
4-1/M82	0.89151	1
4-3-2/M82	0.97091	1
4-3/M82	1.02659	1
5-3/M82	1.02334	1
6-2/M82	1.01433	1
6-3/M82	0.98627	1
7-1/M82	1.09907	1
7-2/M82	0.96361	0.796
9-3-2/M82	1.04128	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.32442	0.277
IL2-6/WTpooled	0.96272	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.06119	1
IL12-4/WTpooled	0.74898	0.566
IL1-4/WTpooled	1.11543	0.426
WT/WTpooled	0.88553	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	0.92652	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06025	0.75
DC3000/delta hrp 6h	0.918	0.95
DC3000/delta hrp 12h	0.95622	1
DC3000/delta hrp 24h	1.25255	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94759	0.955
DC3000 delta B/DC3000 delta AB	1.04806	0.524

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02457	1
Exp 36h	1.09897	1
Exp 60h	1.06126	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97804	1
Var 0h	0.84332	0.933
Var 12h I row2-row1	1.02775	1
Var 12h NI row2-row1	1.0576	1
Var 36h I row2-row1	0.96455	1
Var 36h NI row2-row1	1.1635	1
Var 60h I row2-row1	0.90486	0.582
Var 60h NI row2-row1	1.03257	1
Time course 0hI-0hNI	0.9485	0.617
Time course 12hI-12hNI	0.97798	0.858
Time course 36hI-36hNI	1.00957	0.89
Time course 60hI-60hNI	1.08385	0.302

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)	1.1479	0.232
transgenic ySAMdc/azygous control (breaker)	0.73485	0.15
transgenic ySAMdc/azygous control (red)	1.10749	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00252	0.909

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91077	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74979	1
Manapal/WT (break)	0.83734	1
Manapal/WT (red)	1.35013	0.133