Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.14.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96452	0.699
27DAP/17DAP	2.13612	0.579
39DAP/27DAP	1.01781	0.749
41DAP/39DAP	1.16115	0.915
42DAP/41DAP	1.36581	0.691
43DAP/42DAP	0.75198	0.467
47DAP/43DAP	0.63559	0.148
52DAP/47DAP	3.27709	0.11
57DAP/52DAP	0.62731	0.588

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05282	0.611
17DAP/reference	0.95925	0.321
27DAP/reference	0.94071	0.349
39DAP/reference	0.9664	0.611
41DAP/reference	1.04194	0.241
42DAP/reference	1.19246	0.006
43DAP/reference	0.9546	0.41
47DAP/reference	1.09966	0.448
52DAP/reference	1.0455	0.768
57DAP/reference	1.06614	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89933	0.141
27DAP/17DAP	0.90713	0.58
39DAP/27DAP	1.21314	0.429
41DAP/39DAP	1.09413	0.837
42DAP/41DAP	1.04709	0.947
43DAP/42DAP	1.08092	0.627
47DAP/43DAP	1.06115	0.678
52DAP/47DAP	0.98617	0.925
57DAP/52DAP	0.89211	0.411
57DAP/7DAP	0.82253	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83431	0.091
17DAP/reference	0.86628	0.108
27DAP/reference	1.01691	1
39DAP/reference	0.80968	0.027
41DAP/reference	0.90989	0.122
42DAP/reference	0.96314	0.371
43DAP/reference	0.99612	0.665
47DAP/reference	0.82321	0.033
52DAP/reference	0.84188	0.053
57DAP/reference	0.93609	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20628	0.113
17DAP/reference	1.19744	0.023
27DAP/reference	1.20591	0.092
39DAP/reference	0.91493	0.227
41DAP/reference	0.99634	0.584
42DAP/reference	1.21442	0.022
43DAP/reference	1.44829	0.018
47DAP/reference	1.12575	0.021
52DAP/reference	0.96392	0.407
57DAP/reference	1.33251	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91204	0.268
17DAP/reference	1.13645	0.62
27DAP/reference	1.02677	0.834
39DAP/reference	0.97428	0.43
41DAP/reference	1.15101	0.383
42DAP/reference	1.06245	0.877
43DAP/reference	0.99812	0.827
47DAP/reference	1.07862	0.61
52DAP/reference	0.94483	0.538
57DAP/reference	0.94778	0.372

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88262	0.981
26DAP/20DAP	1.04158	0.875
34DAP/26DAP	1.04569	1
51DAP/34DAP	1.08297	0.795
52DAP/51DAP	0.95254	1
53DAP/52DAP	1.05968	0.723
55DAP/53DAP	1.01247	1
57DAP/55DAP	1.11193	0.793
62DAP/57DAP	0.91545	0.681
68DAP/62DAP	1.11118	1
68DAP/14DAP	0.47875	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95667	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93927
Mature Green Tomato/Ripe Tomato	0.91889	0.446
Immature Eggplant/Mature Eggplant	0.94177
Ripe Pepper/Ripe Tomato	0.7864	1
Mature Eggplant/Ripe Tomato	0.45358	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09804	1
1-1-2/M82	0.9315	1
12-2/M82	1.49252
12-4/M82	1.07954	1
1-3/M82	1.08018	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.13802	0.452
3-2/M82	N/A	N/A
4-1-1/M82	0.70675
4-1/M82	0.84027	1
4-3-2/M82	0.90769	1
4-3/M82	1.2088
5-3/M82	1.01873	1
6-2/M82	0.97906	1
6-3/M82	1.03588	1
7-1/M82	N/A	N/A
7-2/M82	1.00599	1
9-3-2/M82	0.62895

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.04194	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0112	1
IL12-4/WTpooled	0.96723	1
IL1-4/WTpooled	1.0207
WT/WTpooled	0.93916	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03486	0.846
DC3000/delta hrp 6h	1.12882	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.08355	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74266
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	1.28241	1
Exp 36h	0.51874	0.406
Exp 60h	0.66234	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0285	1
Var 0h	0.89154	0.933
Var 12h I row2-row1	1.13915	0.473
Var 12h NI row2-row1	0.88663	0.713
Var 36h I row2-row1	0.79432	0.805
Var 36h NI row2-row1	1.09346	1
Var 60h I row2-row1	1.84543	0.562
Var 60h NI row2-row1	1.13547	0.904
Time course 0hI-0hNI	0.96171	0.755
Time course 12hI-12hNI	0.98549	0.897
Time course 36hI-36hNI	1.01019	0.799
Time course 60hI-60hNI	0.91159	0.161

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)	0.95256	0.314
transgenic ySAMdc/azygous control (breaker)	0.84348	0.142
transgenic ySAMdc/azygous control (red)	1.20485	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01736	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84452	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92633	1
Manapal/WT (break)	0.55734	0.299
Manapal/WT (red)	0.42999	0.181