Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.12.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.76113	0.057
27DAP/17DAP	0.87587	0.602
39DAP/27DAP	1.63183	0.332
41DAP/39DAP	0.75687	0.311
42DAP/41DAP	1.09781	0.958
43DAP/42DAP	1.04966	1
47DAP/43DAP	1.12185	0.856
52DAP/47DAP	1.3301	0.462
57DAP/52DAP	1.04317	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1691	0.081
17DAP/reference	1.07722	0.042
27DAP/reference	1.05917	0.239
39DAP/reference	1.02527	0.504
41DAP/reference	1.17642	0.029
42DAP/reference	1.28433	0.001
43DAP/reference	0.96561	0.594
47DAP/reference	1.16246	0.004
52DAP/reference	1.22996	0.056
57DAP/reference	0.93016	0.277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10041	0.356
27DAP/17DAP	0.97097	0.854
39DAP/27DAP	1.22696	0.147
41DAP/39DAP	1.01502	1
42DAP/41DAP	0.93382	0.545
43DAP/42DAP	0.94866	0.399
47DAP/43DAP	1.04367	0.892
52DAP/47DAP	1.15736	0.498
57DAP/52DAP	1.02778	0.874
57DAP/7DAP	0.98706	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13709	0.292
17DAP/reference	0.71732	0.013
27DAP/reference	0.56709	0.011
39DAP/reference	0.37475	0.011
41DAP/reference	0.39463	0.016
42DAP/reference	0.27683	0.01
43DAP/reference	0.27072	0.009
47DAP/reference	0.64039	0.168
52DAP/reference	0.31712	0.009
57DAP/reference	0.3381	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07287	0.75
17DAP/reference	1.22449	0.027
27DAP/reference	1.2705	0.076
39DAP/reference	1.27133	0.024
41DAP/reference	1.08144	0.599
42DAP/reference	1.16989	0.176
43DAP/reference	1.00387	0.561
47DAP/reference	1.17188	0.034
52DAP/reference	1.16932	0.007
57DAP/reference	1.32286	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.01334	0.016
17DAP/reference	1.65023	0.182
27DAP/reference	1.30462	0.075
39DAP/reference	1.24341	0.032
41DAP/reference	0.71991	0.032
42DAP/reference	0.74092	0.134
43DAP/reference	0.71747	0.092
47DAP/reference	1.03258	0.82
52DAP/reference	0.57078	0.15
57DAP/reference	0.97074	0.572

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93846	1
26DAP/20DAP	1.14845	0.608
34DAP/26DAP	0.98403	0.988
51DAP/34DAP	1.21768	0.293
52DAP/51DAP	1.24419	0.158
53DAP/52DAP	0.94744	0.553
55DAP/53DAP	1.12779	0.394
57DAP/55DAP	0.9889	0.909
62DAP/57DAP	1.11739	0.678
68DAP/62DAP	1.06815	1
68DAP/14DAP	0.92094	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.091	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.91094
Mature Green Tomato/Ripe Tomato	2.09304	0.015
Immature Eggplant/Mature Eggplant	1.69291	0.05
Ripe Pepper/Ripe Tomato	0.57407	0.224
Mature Eggplant/Ripe Tomato	1.19665

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	N/A	N/A
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	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	N/A	N/A
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	0.92459	1
IL2-6/WTpooled	0.97194	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10041	1
IL12-4/WTpooled	1.00048	1
IL1-4/WTpooled	0.97586	0.699
WT/WTpooled	0.97964	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	0.90034	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94563	1
DC3000/delta hrp 6h	0.4903	0.801
DC3000/delta hrp 12h	0.98876	1
DC3000/delta hrp 24h	0.78058	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95861	0.882
DC3000 delta B/DC3000 delta AB	1.01159	0.771

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.82012	1
Exp 36h	N/A	N/A
Exp 60h	1.77573	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96021	1
Var 0h	1.16642	0.594
Var 12h I row2-row1	0.87327	0.357
Var 12h NI row2-row1	1.06569	1
Var 36h I row2-row1	1.04259	1
Var 36h NI row2-row1	0.96699	0.791
Var 60h I row2-row1	1.00523	1
Var 60h NI row2-row1	1.08946	0.904
Time course 0hI-0hNI	0.96553	0.829
Time course 12hI-12hNI	0.99213	0.994
Time course 36hI-36hNI	0.96829	0.46
Time course 60hI-60hNI	0.86724	0.081

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)	1.46864	0.213
transgenic ySAMdc/azygous control (breaker)	0.80064	0.49
transgenic ySAMdc/azygous control (red)	2.38364	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98138	0.149

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.51382	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72345	1
Manapal/WT (break)	0.84974	1
Manapal/WT (red)	0.80785	0.181