Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0894	0.878
27DAP/17DAP	1.31977	0.742
39DAP/27DAP	0.94295	0.537
41DAP/39DAP	1.09407	0.701
42DAP/41DAP	2.63845	0.104
43DAP/42DAP	0.94217	0.786
47DAP/43DAP	0.8346	0.492
52DAP/47DAP	0.90202	0.709
57DAP/52DAP	0.95735	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93038	0.238
17DAP/reference	0.89743	0.208
27DAP/reference	0.94407	0.395
39DAP/reference	0.8377	0.09
41DAP/reference	0.85982	0.018
42DAP/reference	1.00844	0.645
43DAP/reference	0.90529	0.033
47DAP/reference	0.97525	0.418
52DAP/reference	1.04631	0.607
57DAP/reference	1.01215	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29436	0.045
27DAP/17DAP	0.9803	0.878
39DAP/27DAP	1.93527	0.067
41DAP/39DAP	2.47584	0.019
42DAP/41DAP	1.27582	0.663
43DAP/42DAP	0.82099	0.321
47DAP/43DAP	4.08391	0.012
52DAP/47DAP	0.80137	0.585
57DAP/52DAP	2.03494	0.029
57DAP/7DAP	12.3713	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.0661	0.038
17DAP/reference	1.57658	0.01
27DAP/reference	1.14751	0.301
39DAP/reference	1.63738	0.436
41DAP/reference	1.26459	0.048
42DAP/reference	1.63518	0.011
43DAP/reference	1.92615	0.032
47DAP/reference	1.9395	0.019
52DAP/reference	1.84749	0.007
57DAP/reference	1.62913	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69537	0.016
17DAP/reference	0.64337	0.004
27DAP/reference	0.95012	0.407
39DAP/reference	1.20692	0.194
41DAP/reference	1.20021	0.335
42DAP/reference	1.15417	0.136
43DAP/reference	1.24876	0.949
47DAP/reference	1.23968	0.274
52DAP/reference	0.97916	0.5
57DAP/reference	1.46415	0.277

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19887	0.28
17DAP/reference	1.03527	0.918
27DAP/reference	1.28921	0.12
39DAP/reference	1.21959	0.053
41DAP/reference	1.2197	0.024
42DAP/reference	1.07105	0.743
43DAP/reference	1.33694	0.137
47DAP/reference	0.74568	0.038
52DAP/reference	1.09568	0.683
57DAP/reference	1.92644	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.39392	0.817
26DAP/20DAP	0.94333	1
34DAP/26DAP	1.05592	1
51DAP/34DAP	0.93626	0.606
52DAP/51DAP	1.1001	0.387
53DAP/52DAP	1.02291	0.935
55DAP/53DAP	1.31736	0.047
57DAP/55DAP	1.21709	0.348
62DAP/57DAP	0.51296	0.003
68DAP/62DAP	1.32555	0.582
68DAP/14DAP	1.35412	0.108

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.77943	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.60686	0.132
Immature Eggplant/Mature Eggplant	2.97369	0.05
Ripe Pepper/Ripe Tomato	0.0522	0.224
Mature Eggplant/Ripe Tomato	0.33637	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.73719	1
12-2/M82	0.39554
12-4/M82	0.69864	0.619
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.93589
4-1-1/M82	N/A	N/A
4-1/M82	1.21056	1
4-3-2/M82	0.93236	1
4-3/M82	N/A	N/A
5-3/M82	1.42246	0.572
6-2/M82	4.95224
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.39542
9-3-2/M82	0.99265	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.92435	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0795	1
IL12-4/WTpooled	1.12421	0.737
IL1-4/WTpooled	1.05292
WT/WTpooled	0.97507	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	1.20421	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06049	0.921
DC3000/delta hrp 6h	1.267	0.631
DC3000/delta hrp 12h	0.99088	1
DC3000/delta hrp 24h	1.00484	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71208	0.024
DC3000 delta B/DC3000 delta AB	0.87304	0.178

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01298	1
Exp 36h	2.51579	0.489
Exp 60h	1.64184	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96234	1
Var 0h	1.12485	0.782
Var 12h I row2-row1	1.01002	1
Var 12h NI row2-row1	1.37536	0.649
Var 36h I row2-row1	0.69023	0.805
Var 36h NI row2-row1	0.77651	0.329
Var 60h I row2-row1	0.61365	0.285
Var 60h NI row2-row1	1.08889	0.904
Time course 0hI-0hNI	1.09364	0.63
Time course 12hI-12hNI	1.17342	0.354
Time course 36hI-36hNI	2.06331	0.005
Time course 60hI-60hNI	7.38681	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)	1.10408	0.312
transgenic ySAMdc/azygous control (breaker)	0.72831	0.131
transgenic ySAMdc/azygous control (red)	0.91067	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91075	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.54783	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08632	1
Manapal/WT (break)	1.67733	0.123
Manapal/WT (red)	0.70711	0.503