Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.3.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68928	0.137
27DAP/17DAP	0.54882	0.038
39DAP/27DAP	0.92547	0.652
41DAP/39DAP	0.98818	0.802
42DAP/41DAP	1.07985	0.978
43DAP/42DAP	1.10958	1
47DAP/43DAP	0.95717	0.744
52DAP/47DAP	1.23501	0.543
57DAP/52DAP	0.84209	0.71

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05527	0.662
17DAP/reference	0.91835	0.224
27DAP/reference	0.962	0.538
39DAP/reference	0.75796	0.1
41DAP/reference	0.85184	0.021
42DAP/reference	0.82504	0.05
43DAP/reference	1.00849
47DAP/reference	0.93483	0.445
52DAP/reference	0.84606	0.099
57DAP/reference	0.52175

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73121	0.032
27DAP/17DAP	1.23484	0.174
39DAP/27DAP	0.73298	0.029
41DAP/39DAP	0.64286	0.013
42DAP/41DAP	1.06819	0.753
43DAP/42DAP	1.31854	0.016
47DAP/43DAP	0.89183	0.297
52DAP/47DAP	0.92453	0.71
57DAP/52DAP	0.84144	0.299
57DAP/7DAP	0.50858	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13947	0.121
17DAP/reference	0.94318	0.124
27DAP/reference	0.82981	0.01
39DAP/reference	0.75164	0.011
41DAP/reference	0.72847	0.011
42DAP/reference	0.69991	0.01
43DAP/reference	0.73224	0.02
47DAP/reference	0.77392	0.128
52DAP/reference	0.78114	0.017
57DAP/reference	0.73573	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15359	0.111
17DAP/reference	1.30616	0.026
27DAP/reference	1.23008	0.022
39DAP/reference	0.87956	0.069
41DAP/reference	0.92363	0.121
42DAP/reference	0.95032	0.355
43DAP/reference	1.05305	0.515
47DAP/reference	0.90632	0.069
52DAP/reference	1.02248	0.938
57DAP/reference	1.09326	0.26

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40098	0.015
17DAP/reference	1.15736	0.117
27DAP/reference	1.04635	0.408
39DAP/reference	0.87309	0.043
41DAP/reference	0.88007	0.023
42DAP/reference	0.91873	0.134
43DAP/reference	0.84467	0.033
47DAP/reference	0.98334	0.525
52DAP/reference	0.7516	0.068
57DAP/reference	0.73754	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90716	0.915
26DAP/20DAP	1.33083	0.168
34DAP/26DAP	0.9754	0.961
51DAP/34DAP	1.34611	0.064
52DAP/51DAP	0.8951	1
53DAP/52DAP	0.8486	0.221
55DAP/53DAP	0.6324	0.02
57DAP/55DAP	0.75037	0.135
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.87074	0.747
68DAP/14DAP	0.78156	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.17809	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.49138	0.058
Mature Green Tomato/Ripe Tomato	6.0195	0.015
Immature Eggplant/Mature Eggplant	0.27817	0.057
Ripe Pepper/Ripe Tomato	29.2834	0.256
Mature Eggplant/Ripe Tomato	15.5822	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95887	0.961
1-1-2/M82	0.99169	1
12-2/M82	1.04193	1
12-4/M82	1.02581	1
1-3/M82	0.91596	0.378
2-1-1/M82	0.90586
2-1/M82	0.78882	0.519
2-6/M82	1.1178	0.695
3-2/M82	0.90899
4-1-1/M82	1.03791	1
4-1/M82	1.18539
4-3-2/M82	1.14633
4-3/M82	1.19159	1
5-3/M82	0.92354	1
6-2/M82	N/A	N/A
6-3/M82	1.11768	0.971
7-1/M82	0.76841
7-2/M82	1.00658	1
9-3-2/M82	0.68304

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.66797	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.091	1
IL1-4/WTpooled	1.12425	1
WT/WTpooled	1.21692

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	0.84008	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95251	1
DC3000/delta hrp 6h	0.99271	0.95
DC3000/delta hrp 12h	1.04001	1
DC3000/delta hrp 24h	0.574	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.39176	0.023
DC3000 delta B/DC3000 delta AB	0.45111	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85487	0.328
Exp 36h	0.75821	0.406
Exp 60h	0.57163	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02444	1
Var 0h	0.91064	0.933
Var 12h I row2-row1	0.74455	0.338
Var 12h NI row2-row1	0.91062	0.33
Var 36h I row2-row1	0.87165	0.805
Var 36h NI row2-row1	1.35003	0.482
Var 60h I row2-row1	1.12765	0.562
Var 60h NI row2-row1	1.08695	0.904
Time course 0hI-0hNI	0.9636	0.702
Time course 12hI-12hNI	1.01346	0.836
Time course 36hI-36hNI	0.77416	0.023
Time course 60hI-60hNI	0.15499	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)	0.86599	0.314
transgenic ySAMdc/azygous control (breaker)	0.95984	1
transgenic ySAMdc/azygous control (red)	2.8354	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94637	0.053

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.55194	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.5809	0.14
Manapal/WT (break)	2.96406	0.183
Manapal/WT (red)	2.17601	0.142