Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36661	0.575
27DAP/17DAP	1.69551	0.646
39DAP/27DAP	1.05531	1
41DAP/39DAP	1.57741	0.728
42DAP/41DAP	1.02995	1
43DAP/42DAP	1.08247	0.937
47DAP/43DAP	1.43292	0.555
52DAP/47DAP	1.14342	0.758
57DAP/52DAP	1.0374	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05993	0.76
17DAP/reference	0.99248	0.858
27DAP/reference	1.08117	0.435
39DAP/reference	1.00473	0.975
41DAP/reference	1.06174	0.451
42DAP/reference	0.93929	0.115
43DAP/reference	0.92026	0.17
47DAP/reference	0.96627	0.366
52DAP/reference	0.95674	0.405
57DAP/reference	0.98725	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.97299	0.5
27DAP/17DAP	1.71738	0.264
39DAP/27DAP	1.20207	0.672
41DAP/39DAP	1.05467	0.914
42DAP/41DAP	0.87688	0.469
43DAP/42DAP	1.47569	0.585
47DAP/43DAP	1.14084	0.914
52DAP/47DAP	1.00436	0.93
57DAP/52DAP	1.83959	0.188
57DAP/7DAP	1.38233

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06693	0.427
17DAP/reference	1.24044	0.038
27DAP/reference	1.12971	0.16
39DAP/reference	1.44641	0.007
41DAP/reference	1.34588	0.01
42DAP/reference	1.36476	0.016
43DAP/reference	1.45713	0.014
47DAP/reference	0.92121	0.504
52DAP/reference	1.11786	0.183
57DAP/reference	1.28853	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82995	0.058
17DAP/reference	0.82985	0.07
27DAP/reference	0.76111	0.06
39DAP/reference	0.87267	0.14
41DAP/reference	0.92638	0.268
42DAP/reference	0.86629	0.108
43DAP/reference	0.82815	0.095
47DAP/reference	0.92461	0.168
52DAP/reference	0.75808	0.009
57DAP/reference	0.73689	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21235	0.024
17DAP/reference	1.06274	0.792
27DAP/reference	1.34639	0.027
39DAP/reference	1.26884	0.011
41DAP/reference	1.17215	0.096
42DAP/reference	1.22188	0.199
43DAP/reference	1.06176	0.599
47DAP/reference	0.94902	0.335
52DAP/reference	1.2851	0.128
57DAP/reference	1.05645	0.867

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14509	0.916
26DAP/20DAP	0.76378	1
34DAP/26DAP	0.95432	0.998
51DAP/34DAP	1.45169	0.281
52DAP/51DAP	1.11519	0.954
53DAP/52DAP	1.44145	0.895
55DAP/53DAP	0.78884	0.313
57DAP/55DAP	1.38994	0.71
62DAP/57DAP	0.88908	0.871
68DAP/62DAP	0.90251	0.641
68DAP/14DAP	1.24822	0.103

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04607	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.63815
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.36471
Mature Eggplant/Ripe Tomato	0.62057

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31991
1-1-2/M82	1.03777
12-2/M82	N/A	N/A
12-4/M82	0.8648
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	1.198
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	0.96582	1
6-2/M82	N/A	N/A
6-3/M82	0.9822
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	1.33302	0.277
IL2-6/WTpooled	1.65971	0.395
IL7-5/WTpooled	1.12105	1
IL7-3/WTpooled	0.78967	0.31
IL12-4/WTpooled	1.22174	0.839
IL1-4/WTpooled	1.15667	1
WT/WTpooled	1.03255	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	0.90118

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92732	1
DC3000/delta hrp 6h	1.05646	0.95
DC3000/delta hrp 12h	0.93098	1
DC3000/delta hrp 24h	0.83019	0.09

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83197	1
Exp 36h	0.91142	0.749
Exp 60h	0.71324	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96265	1
Var 0h	0.77406
Var 12h I row2-row1	1.11877	0.272
Var 12h NI row2-row1	1.24059
Var 36h I row2-row1	0.90696	0.805
Var 36h NI row2-row1	0.92937	0.276
Var 60h I row2-row1	0.94035	0.582
Var 60h NI row2-row1	1.22622	0.691
Time course 0hI-0hNI	0.92277	0.595
Time course 12hI-12hNI	0.95164	0.725
Time course 36hI-36hNI	0.78214	0.023
Time course 60hI-60hNI	0.31094	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)	0.93579	0.314
transgenic ySAMdc/azygous control (breaker)	1.21597	0.178
transgenic ySAMdc/azygous control (red)	1.16738	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96187	0.131

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.48524	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32156	0.096
Manapal/WT (break)	0.95479	1
Manapal/WT (red)	1.81729	0.134