Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.5.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97726	0.596
27DAP/17DAP	0.63451	0.105
39DAP/27DAP	1.75861	0.305
41DAP/39DAP	1.02041	1
42DAP/41DAP	1.34063	0.877
43DAP/42DAP	1.14506	0.831
47DAP/43DAP	1.09035	0.943
52DAP/47DAP	0.82247	0.619
57DAP/52DAP	0.77238	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98787	0.661
17DAP/reference	0.75404	0.018
27DAP/reference	0.79442	0.134
39DAP/reference	0.71622	0.038
41DAP/reference	0.68666	0.039
42DAP/reference	0.73322	0.007
43DAP/reference	0.89134	0.247
47DAP/reference	0.79088	0.007
52DAP/reference	0.71474	0.029
57DAP/reference	0.865	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.37262	0.03
27DAP/17DAP	1.58237	0.05
39DAP/27DAP	0.47015	0.03
41DAP/39DAP	0.3655	0.013
42DAP/41DAP	1.33744	0.795
43DAP/42DAP	1.64378	0.03
47DAP/43DAP	0.91843	0.647
52DAP/47DAP	0.97957	0.907
57DAP/52DAP	0.76602	0.484
57DAP/7DAP	0.25156	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95856	0.495
17DAP/reference	0.98755	0.599
27DAP/reference	1.05073	0.974
39DAP/reference	1.04205	1
41DAP/reference	0.71982	0.05
42DAP/reference	0.80504	0.066
43DAP/reference	1.12766	0.788
47DAP/reference	0.76774	0.168
52DAP/reference	0.96872	0.477
57DAP/reference	0.85561	0.045

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83847	0.257
17DAP/reference	0.94717	0.487
27DAP/reference	0.96498	0.423
39DAP/reference	0.70885	0.071
41DAP/reference	0.93197	0.331
42DAP/reference	0.80146	0.039
43DAP/reference	0.72608	0.034
47DAP/reference	0.65384	0.012
52DAP/reference	0.57816	0.047
57DAP/reference	0.69053	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02769	0.75
17DAP/reference	1.00593	0.81
27DAP/reference	0.91993	0.206
39DAP/reference	0.87819	0.024
41DAP/reference	0.93933	0.459
42DAP/reference	0.80286	0.087
43DAP/reference	0.93054	0.319
47DAP/reference	0.57566	0.005
52DAP/reference	2.56623	0.735
57DAP/reference	1.03463	0.693

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.78389	1
26DAP/20DAP	1.05689	0.953
34DAP/26DAP	0.78486	0.148
51DAP/34DAP	0.58235	0.049
52DAP/51DAP	1.04967	0.708
53DAP/52DAP	0.83686	0.202
55DAP/53DAP	0.48313	0.019
57DAP/55DAP	0.80491	0.318
62DAP/57DAP	0.91731	0.994
68DAP/62DAP	1.01249	0.971
68DAP/14DAP	0.76384	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.13561	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.96091	0.058
Mature Green Tomato/Ripe Tomato	3.00591	0.015
Immature Eggplant/Mature Eggplant	0.60049	0.092
Ripe Pepper/Ripe Tomato	0.91425
Mature Eggplant/Ripe Tomato	4.37234	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17404
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.08549
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.84601
2-6/M82	N/A	N/A
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	N/A	N/A
5-3/M82	0.99595	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.1866
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09712	0.277
IL2-6/WTpooled	1.73759	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.8983	0.418
IL12-4/WTpooled	0.9788	1
IL1-4/WTpooled	0.93783	1
WT/WTpooled	0.83992	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	0.90368	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87747	0.941
DC3000/delta hrp 6h	1.0463	0.95
DC3000/delta hrp 12h	0.98594	1
DC3000/delta hrp 24h	0.72498	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.36938	0.023
DC3000 delta B/DC3000 delta AB	0.43709	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06354	1
Exp 36h	0.69097	0.406
Exp 60h	0.60956	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03773	1
Var 0h	1.12251	0.594
Var 12h I row2-row1	0.76057	0.338
Var 12h NI row2-row1	0.96038	0.906
Var 36h I row2-row1	1.19531	0.908
Var 36h NI row2-row1	1.29757	1
Var 60h I row2-row1	0.89196	0.832
Var 60h NI row2-row1	1.02554	1
Time course 0hI-0hNI	1.06265	0.63
Time course 12hI-12hNI	0.93781	0.592
Time course 36hI-36hNI	0.75386	0.035
Time course 60hI-60hNI	0.10713	0.005

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)	0.94319	0.428
transgenic ySAMdc/azygous control (breaker)	1.30357	0.178
transgenic ySAMdc/azygous control (red)	1.04803	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7702	0.099

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.89676	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.38453	0.084
Manapal/WT (break)	1.82046	0.381
Manapal/WT (red)	1.06483	1