Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.9.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.49843	0.016
27DAP/17DAP	0.9263	0.831
39DAP/27DAP	1.54601	0.148
41DAP/39DAP	0.70491	0.086
42DAP/41DAP	1.11558	0.938
43DAP/42DAP	1.10176	0.993
47DAP/43DAP	0.98477	0.902
52DAP/47DAP	1.89608	0.238
57DAP/52DAP	1.08997	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31318	0.012
17DAP/reference	0.9023	0.278
27DAP/reference	0.77532	0.013
39DAP/reference	0.95559	0.513
41DAP/reference	0.78617	0.085
42DAP/reference	1.05867	0.352
43DAP/reference	0.97561	0.708
47DAP/reference	1.48704	0.018
52DAP/reference	1.90726	0.008
57DAP/reference	1.14291	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66896	0.03
27DAP/17DAP	1.25829	0.09
39DAP/27DAP	0.88681	0.235
41DAP/39DAP	0.89508	0.662
42DAP/41DAP	1.0986	0.478
43DAP/42DAP	1.07522	0.382
47DAP/43DAP	1.03917	0.873
52DAP/47DAP	0.93348	0.624
57DAP/52DAP	1.02336	0.891
57DAP/7DAP	0.8952	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.57689	0.025
17DAP/reference	1.60538	0.009
27DAP/reference	1.53752	0.006
39DAP/reference	1.13395	0.036
41DAP/reference	1.59117	0.012
42DAP/reference	1.755	0.009
43DAP/reference	1.66466	0.006
47DAP/reference	1.2703	0.028
52DAP/reference	1.9184	0.009
57DAP/reference	1.41825	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39355	0.187
17DAP/reference	1.15652	0.065
27DAP/reference	1.22738	0.118
39DAP/reference	0.83041	0.089
41DAP/reference	1.05631	0.427
42DAP/reference	1.14137	0.039
43DAP/reference	0.87424	0.175
47DAP/reference	1.16088	0.011
52DAP/reference	0.7804	0.004
57DAP/reference	0.80344	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.35809	0.015
17DAP/reference	1.32494	0.07
27DAP/reference	1.34027	0.022
39DAP/reference	1.40398	0.008
41DAP/reference	1.06492	0.156
42DAP/reference	1.27647	0.097
43DAP/reference	1.17023	0.302
47DAP/reference	0.88938	0.041
52DAP/reference	1.8769	0.029
57DAP/reference	1.82499	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88512	1
26DAP/20DAP	1.13549	0.404
34DAP/26DAP	0.93784	0.712
51DAP/34DAP	0.93944	0.508
52DAP/51DAP	1.06172	0.387
53DAP/52DAP	1.009	0.944
55DAP/53DAP	0.98563	0.838
57DAP/55DAP	1.01463	0.955
62DAP/57DAP	1.16336	0.217
68DAP/62DAP	0.92562	0.747
68DAP/14DAP	0.67473	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.37979	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23624	0.063
Mature Green Tomato/Ripe Tomato	0.6919	0.317
Immature Eggplant/Mature Eggplant	0.91117	0.117
Ripe Pepper/Ripe Tomato	0.3588	0.224
Mature Eggplant/Ripe Tomato	0.4067	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06793	1
1-1-2/M82	1.1832	1
12-2/M82	1.03697	1
12-4/M82	1.24671	1
1-3/M82	1.9116	0.255
2-1-1/M82	1.00199	1
2-1/M82	0.77596	0.322
2-6/M82	1.11155	0.594
3-2/M82	1.26031	0.717
4-1-1/M82	0.74524	1
4-1/M82	1.38345	0.853
4-3-2/M82	1.5483	0.241
4-3/M82	1.35832	0.268
5-3/M82	1.20405	1
6-2/M82	1.09273
6-3/M82	1.04636	1
7-1/M82	0.83288	0.803
7-2/M82	1.2082	0.318
9-3-2/M82	1.24372	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.10978	0.365
IL2-6/WTpooled	0.98235	1
IL7-5/WTpooled	1.15826	1
IL7-3/WTpooled	0.9588	0.418
IL12-4/WTpooled	1.12745	0.503
IL1-4/WTpooled	0.97614	0.834
WT/WTpooled	0.96923	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	0.9704	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05568	0.921
DC3000/delta hrp 6h	1.08273	1
DC3000/delta hrp 12h	1.06204	1
DC3000/delta hrp 24h	0.84779	0.08

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12391	0.087
DC3000 delta B/DC3000 delta AB	1.12483	0.304

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94856	1
Exp 36h	1.5271	0.326
Exp 60h	1.6541	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02102	1
Var 0h	0.80543	0.339
Var 12h I row2-row1	1.17067	0.692
Var 12h NI row2-row1	1.05595	1
Var 36h I row2-row1	1.17529	0.908
Var 36h NI row2-row1	0.80893	0.378
Var 60h I row2-row1	0.8878	0.287
Var 60h NI row2-row1	0.91017	0.866
Time course 0hI-0hNI	0.99621	1
Time course 12hI-12hNI	1.04646	0.554
Time course 36hI-36hNI	1.74758	0.004
Time course 60hI-60hNI	5.09594	0.008

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)	1.16733	0.612
transgenic ySAMdc/azygous control (breaker)	1.14304	1
transgenic ySAMdc/azygous control (red)	1.08738	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10181	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64935	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16709	0.105
Manapal/WT (break)	1.24694	0.381
Manapal/WT (red)	1.13448	0.222