Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.57565	0.037
27DAP/17DAP	0.3512	0.024
39DAP/27DAP	0.68566	0.312
41DAP/39DAP	1.12595	0.735
42DAP/41DAP	0.76422	0.774
43DAP/42DAP	0.68485	0.708
47DAP/43DAP	1.19223	0.727
52DAP/47DAP	0.64927	0.179
57DAP/52DAP	1.12709	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4296	0.093
17DAP/reference	0.3423	0.008
27DAP/reference	0.30293	0.011
39DAP/reference	0.33719	0.01
41DAP/reference	0.24976	0.008
42DAP/reference	0.35478	0.001
43DAP/reference	0.23933	0.012
47DAP/reference	0.35496	0.001
52DAP/reference	0.29253	0.013
57DAP/reference	0.31012	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.31895	0.033
27DAP/17DAP	1.07359	0.852
39DAP/27DAP	0.98685	0.943
41DAP/39DAP	1.13555	0.753
42DAP/41DAP	0.75525	0.056
43DAP/42DAP	0.75609	0.079
47DAP/43DAP	0.9091	0.637
52DAP/47DAP	0.77655	0.304
57DAP/52DAP	0.99688	0.773
57DAP/7DAP	0.4528	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67947	0.039
17DAP/reference	0.6715	0.012
27DAP/reference	0.52624	0.01
39DAP/reference	0.50106	0.011
41DAP/reference	0.90695	0.235
42DAP/reference	0.51724	0.01
43DAP/reference	0.51995	0.011
47DAP/reference	0.35879	0.044
52DAP/reference	0.47023	0.009
57DAP/reference	0.40962	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16174	0.612
17DAP/reference	0.35641	0.003
27DAP/reference	0.37918	0.012
39DAP/reference	0.23771	0.008
41DAP/reference	0.56791	0.022
42DAP/reference	0.3497	0.011
43DAP/reference	0.26412	0.002
47DAP/reference	0.4107	0.008
52DAP/reference	0.23659	0.003
57DAP/reference	0.32659	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46668	0.493
17DAP/reference	0.71944	0.189
27DAP/reference	0.5087	0.025
39DAP/reference	0.45037	0.014
41DAP/reference	0.48508	0.019
42DAP/reference	0.44412	0.016
43DAP/reference	0.3831	0.032
47DAP/reference	0.12555	0.002
52DAP/reference	0.39498	0.075
57DAP/reference	0.29046	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.48563	0.966
26DAP/20DAP	1.24951
34DAP/26DAP	0.612	0.05
51DAP/34DAP	1.25189	0.795
52DAP/51DAP	1.09327	0.792
53DAP/52DAP	0.84526	0.621
55DAP/53DAP	0.99138	0.886
57DAP/55DAP	0.85094	0.468
62DAP/57DAP	1.13023	1
68DAP/62DAP	1.35347	0.616
68DAP/14DAP	1.12856	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06299	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	15.9556	0.023
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.54461
Mature Eggplant/Ripe Tomato	2.08452	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.20916
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	0.86546
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	0.9342	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	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99834	1
IL2-6/WTpooled	0.93488	1
IL7-5/WTpooled	0.84967	1
IL7-3/WTpooled	0.89655	0.31
IL12-4/WTpooled	0.86709	0.71
IL1-4/WTpooled	1.16553	1
WT/WTpooled	1.01086	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	0.94212	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88706	0.868
DC3000/delta hrp 6h	1.1311	1
DC3000/delta hrp 12h	0.33127	1
DC3000/delta hrp 24h	4.16342	0.077

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00219	0.648
DC3000 delta B/DC3000 delta AB	1.05915	0.55

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.31863	1
Exp 36h	N/A	N/A
Exp 60h	1.31304	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97462	1
Var 0h	1.04724	0.98
Var 12h I row2-row1	0.97242	0.948
Var 12h NI row2-row1	0.66361	0.488
Var 36h I row2-row1	1.06754	1
Var 36h NI row2-row1	0.8213	0.645
Var 60h I row2-row1	0.8454	0.832
Var 60h NI row2-row1	0.87979	0.932
Time course 0hI-0hNI	0.96113	0.799
Time course 12hI-12hNI	0.94866	0.739
Time course 36hI-36hNI	1.03668	1
Time course 60hI-60hNI	0.94716	0.646

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)	1.13732	0.798
transgenic ySAMdc/azygous control (breaker)	1.05057	1
transgenic ySAMdc/azygous control (red)	1.21397	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92165	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.81282	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.46805	0.093
Manapal/WT (break)	1.05799	1
Manapal/WT (red)	3.59182	0.137