Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-6.2.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90244	0.464
27DAP/17DAP	0.74017	0.29
39DAP/27DAP	1.29905	0.693
41DAP/39DAP	0.79802	0.291
42DAP/41DAP	1.0031	1
43DAP/42DAP	0.95674	0.877
47DAP/43DAP	1.09484	0.842
52DAP/47DAP	0.90127	0.637
57DAP/52DAP	1.12805	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69001	0.024
17DAP/reference	0.85997	0.06
27DAP/reference	0.85338	0.057
39DAP/reference	0.78661	0.068
41DAP/reference	0.72314	0.018
42DAP/reference	0.79325	0.043
43DAP/reference	3.60899	0.425
47DAP/reference	0.81752	0.008
52DAP/reference	1.00076	0.749
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.47567	0.03
27DAP/17DAP	1.39243	0.07
39DAP/27DAP	0.64508	0.069
41DAP/39DAP	0.74015	0.064
42DAP/41DAP	0.96774	0.717
43DAP/42DAP	1.11406	0.212
47DAP/43DAP	0.93347	0.617
52DAP/47DAP	0.94199	0.763
57DAP/52DAP	1.0101	1
57DAP/7DAP	0.54647	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.35322	0.06
17DAP/reference	0.40174	0.011
27DAP/reference	0.42852	0.01
39DAP/reference	0.24371	0.011
41DAP/reference	0.29933	0.015
42DAP/reference	0.26198	0.01
43DAP/reference	0.26227	0.009
47DAP/reference	0.71816	0.222
52DAP/reference	0.28074	0.009
57DAP/reference	0.35102	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70118	0.014
17DAP/reference	0.65974	0.003
27DAP/reference	1.03735	0.988
39DAP/reference	1.00032	0.621
41DAP/reference	0.94254	0.284
42DAP/reference	0.93348	0.289
43DAP/reference	0.73775	0.036
47DAP/reference	0.78685	0.011
52DAP/reference	0.98456	0.537
57DAP/reference	0.69071	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.41739	0.028
17DAP/reference	0.77906	0.205
27DAP/reference	0.45406	0.03
39DAP/reference	0.45499	0.01
41DAP/reference	0.42948	0.02
42DAP/reference	0.65448	0.134
43DAP/reference	0.69633	0.092
47DAP/reference	0.97841	0.509
52DAP/reference	0.50383	0.082
57DAP/reference	1.21521	0.592

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.79225	0.379
26DAP/20DAP	1.06143	0.839
34DAP/26DAP	0.98998	1
51DAP/34DAP	0.65901	0.059
52DAP/51DAP	1.10598	0.492
53DAP/52DAP	0.84584	0.281
55DAP/53DAP	0.82879	0.149
57DAP/55DAP	0.74971	0.157
62DAP/57DAP	2.27218	0.767
68DAP/62DAP	1.50243	0.132
68DAP/14DAP	2.58632	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.32878	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.86445	0.058
Mature Green Tomato/Ripe Tomato	2.21438	0.02
Immature Eggplant/Mature Eggplant	2.16701	N/A
Ripe Pepper/Ripe Tomato	0.32277	0.224
Mature Eggplant/Ripe Tomato	0.21806	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.04955	0.574
1-1-2/M82	1.26726	1
12-2/M82	1.3391	1
12-4/M82	1.25633	1
1-3/M82	2.63735	0.26
2-1-1/M82	1.06759	1
2-1/M82	0.9508	N/A
2-6/M82	0.79241	1
3-2/M82	0.92494	N/A
4-1-1/M82	0.82761	1
4-1/M82	1.07428	1
4-3-2/M82	1.02667	1
4-3/M82	1.58398	1
5-3/M82	1.11111	0.572
6-2/M82	1.99096	N/A
6-3/M82	1.03909	1
7-1/M82	0.7454	0.803
7-2/M82	1.07822	1
9-3-2/M82	1.13395	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.38362	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.71063	N/A
IL7-3/WTpooled	0.72293	N/A
IL12-4/WTpooled	0.88228	0.71
IL1-4/WTpooled	1.02373	1
WT/WTpooled	1.41945	0.874

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	0.83707	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02009	0.921
DC3000/delta hrp 6h	1.32876	N/A
DC3000/delta hrp 12h	1.59502	1
DC3000/delta hrp 24h	0.61562	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51974	0.023
DC3000 delta B/DC3000 delta AB	0.51809	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99632	1
Var 0h	1.00626	N/A
Var 12h I row2-row1	0.84221	N/A
Var 12h NI row2-row1	0.93521	N/A
Var 36h I row2-row1	1.123	0.309
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.08414	0.227
Time course 12hI-12hNI	0.96201	0.808
Time course 36hI-36hNI	0.82345	0.023
Time course 60hI-60hNI	0.235	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)	0.87761	0.315
transgenic ySAMdc/azygous control (breaker)	0.95909	1
transgenic ySAMdc/azygous control (red)	0.93919	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03435	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97805	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.495	0.307
Manapal/WT (break)	0.86373	1
Manapal/WT (red)	0.78311	0.181