Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.3.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04664	0.911
27DAP/17DAP	1.06792	0.973
39DAP/27DAP	0.55974	0.458
41DAP/39DAP	1.61233	0.504
42DAP/41DAP	1.28502	0.938
43DAP/42DAP	1.89231	0.937
47DAP/43DAP	1.25071	0.773
52DAP/47DAP	1.93622	0.613
57DAP/52DAP	1.31672	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67204	0.024
17DAP/reference	0.63565	0.011
27DAP/reference	0.69107	0.012
39DAP/reference	0.58699	0.02
41DAP/reference	0.5837	0.039
42DAP/reference	3.599	0.001
43DAP/reference	2.24771
47DAP/reference	3.15065	0.148
52DAP/reference	1.19847	0.04
57DAP/reference	0.5324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93072	0.47
27DAP/17DAP	1.03787	0.881
39DAP/27DAP	1.20533	0.108
41DAP/39DAP	1.00114	1
42DAP/41DAP	1.12749	0.446
43DAP/42DAP	2.0078	0.013
47DAP/43DAP	0.86784	0.057
52DAP/47DAP	0.78164	0.042
57DAP/52DAP	0.86604	0.211
57DAP/7DAP	1.0114	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8481	0.138
17DAP/reference	0.79505	0.011
27DAP/reference	0.88221	0.03
39DAP/reference	0.7246	0.011
41DAP/reference	0.87315	0.107
42DAP/reference	0.99865	0.675
43DAP/reference	1.33154	0.028
47DAP/reference	1.33178	0.019
52DAP/reference	0.80824	0.033
57DAP/reference	0.67556	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65933	0.01
17DAP/reference	0.80231	0.056
27DAP/reference	0.92609	0.352
39DAP/reference	0.92683	0.281
41DAP/reference	0.8778	0.156
42DAP/reference	1.08093	0.723
43DAP/reference	0.85335	0.229
47DAP/reference	0.98193	0.527
52DAP/reference	0.75	0.006
57DAP/reference	0.77518	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68346	0.04
17DAP/reference	0.77377	0.102
27DAP/reference	0.78503	0.025
39DAP/reference	0.78042	0.01
41DAP/reference	0.72994	0.018
42DAP/reference	1.64359	0.007
43DAP/reference	2.1573	0.006
47DAP/reference	1.32491	0.077
52DAP/reference	1.55912	0.039
57DAP/reference	1.28117	0.274

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99352	1
26DAP/20DAP	1.2053	0.886
34DAP/26DAP	0.93093	0.811
51DAP/34DAP	1.08845	0.597
52DAP/51DAP	0.82779	0.064
53DAP/52DAP	1.34089	0.085
55DAP/53DAP	0.95169	0.709
57DAP/55DAP	1.29	0.682
62DAP/57DAP	0.26025
68DAP/62DAP	0.68145	0.101
68DAP/14DAP	1.67096	0.044

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.65351	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.48914	0.088
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.02213
Ripe Pepper/Ripe Tomato	1.28131	1
Mature Eggplant/Ripe Tomato	0.25368	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.32891	0.536
1-1-2/M82	1.30792	1
12-2/M82	1.0689	1
12-4/M82	0.87954	0.358
1-3/M82	2.38601	1
2-1-1/M82	0.59623
2-1/M82	0.61383
2-6/M82	2.17957	0.329
3-2/M82	0.32264
4-1-1/M82	0.555
4-1/M82	0.34387
4-3-2/M82	1.38155
4-3/M82	1.55084	0.268
5-3/M82	0.79671	0.642
6-2/M82	N/A	N/A
6-3/M82	1.04963	1
7-1/M82	0.86018
7-2/M82	2.14124	0.302
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05503	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.32016	0.67
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.92956	1
IL1-4/WTpooled	1.26552	1
WT/WTpooled	1.02716	0.85

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	1.12837	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93558	1
DC3000/delta hrp 6h	0.98893	0.95
DC3000/delta hrp 12h	0.94664	1
DC3000/delta hrp 24h	2.85057	0.024

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24383	0.057
DC3000 delta B/DC3000 delta AB	1.18239	0.19

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.43474	1
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	0.9954	1
Var 0h	1.01908	1
Var 12h I row2-row1	0.92557	0.77
Var 12h NI row2-row1	0.89715	0.713
Var 36h I row2-row1	0.91415	1
Var 36h NI row2-row1	0.90406	0.706
Var 60h I row2-row1	0.98802	1
Var 60h NI row2-row1	1.00195	1
Time course 0hI-0hNI	1.01165	1
Time course 12hI-12hNI	1.13113	0.233
Time course 36hI-36hNI	1.57007	0.005
Time course 60hI-60hNI	1.94069	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)	1.09702	0.372
transgenic ySAMdc/azygous control (breaker)	2.23662	0.172
transgenic ySAMdc/azygous control (red)	1.13554	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09059	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92174	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87985	1
Manapal/WT (break)	1.24896	1
Manapal/WT (red)	1.1191	0.15