Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17334	0.77
27DAP/17DAP	1.2051	0.847
39DAP/27DAP	0.67008	0.397
41DAP/39DAP	1.68611	0.376
42DAP/41DAP	1.01341	1
43DAP/42DAP	1.15736	1
47DAP/43DAP	1.01693	0.868
52DAP/47DAP	1.2688	0.61
57DAP/52DAP	1.12236	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98733	0.63
17DAP/reference	1.0506	0.071
27DAP/reference	1.04093	0.394
39DAP/reference	0.97666	0.734
41DAP/reference	1.05453	0.158
42DAP/reference	0.93782	0.015
43DAP/reference	0.98273	0.728
47DAP/reference	0.91861	0.021
52DAP/reference	0.87964	0.046
57DAP/reference	0.9017	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98389	0.679
27DAP/17DAP	1.03225	0.885
39DAP/27DAP	1.03728	0.575
41DAP/39DAP	1.0658	0.773
42DAP/41DAP	0.95853	0.641
43DAP/42DAP	1.00369	0.83
47DAP/43DAP	0.97831	0.833
52DAP/47DAP	1.00691	0.979
57DAP/52DAP	0.99309	0.848
57DAP/7DAP	0.9969	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92801	0.108
17DAP/reference	0.99576	0.693
27DAP/reference	0.89985	0.023
39DAP/reference	1.04459	0.297
41DAP/reference	1.02498	0.701
42DAP/reference	1.03231	0.534
43DAP/reference	1.11539	0.031
47DAP/reference	0.93086	0.222
52DAP/reference	0.96497	0.232
57DAP/reference	0.9795	0.494

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93654	0.197
17DAP/reference	0.9142	0.095
27DAP/reference	0.88115	0.111
39DAP/reference	0.92388	0.208
41DAP/reference	0.90583	0.137
42DAP/reference	0.93641	0.321
43DAP/reference	0.98136	0.657
47DAP/reference	0.98728	0.574
52DAP/reference	0.96683	0.38
57DAP/reference	1.03249	0.508

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97268	0.335
17DAP/reference	0.98378	0.636
27DAP/reference	0.97514	0.319
39DAP/reference	0.96998	0.36
41DAP/reference	0.96406	0.512
42DAP/reference	0.85633	0.071
43DAP/reference	0.87854	0.106
47DAP/reference	0.95352	0.325
52DAP/reference	0.97432	0.675
57DAP/reference	0.78474	0.057

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01056	0.966
26DAP/20DAP	0.90239	0.228
34DAP/26DAP	1.03749	1
51DAP/34DAP	0.91611	0.385
52DAP/51DAP	0.97695	1
53DAP/52DAP	0.97272	0.862
55DAP/53DAP	0.95663	0.604
57DAP/55DAP	1.25168	0.203
62DAP/57DAP	1.04161	0.833
68DAP/62DAP	0.91737	0.609
68DAP/14DAP	0.71613	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97611	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.78044	0.2
Immature Eggplant/Mature Eggplant	1.14775
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98085	0.961
1-1-2/M82	0.97289	1
12-2/M82	1.02399	1
12-4/M82	0.79917	1
1-3/M82	0.86356	0.501
2-1-1/M82	1.17764	0.457
2-1/M82	N/A	N/A
2-6/M82	0.95666	1
3-2/M82	1.00569	1
4-1-1/M82	0.85761	1
4-1/M82	0.95112	1
4-3-2/M82	0.86692	1
4-3/M82	1.00289	1
5-3/M82	0.91367	0.447
6-2/M82	0.89544	1
6-3/M82	0.99466	1
7-1/M82	1.06457	0.992
7-2/M82	1.1837	1
9-3-2/M82	0.82623	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27497	0.277
IL2-6/WTpooled	0.97198	1
IL7-5/WTpooled	1.03534	1
IL7-3/WTpooled	1.01485	1
IL12-4/WTpooled	1.01428	1
IL1-4/WTpooled	1.22175	1
WT/WTpooled	0.9802	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	1.03904	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.92801	1
DC3000/delta hrp 24h	1.02084	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12053	0.11
DC3000 delta B/DC3000 delta AB	1.0564	0.479

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96313	1
Var 0h	2.57127	0.98
Var 12h I row2-row1	1.10681	0.283
Var 12h NI row2-row1	0.89002	0.438
Var 36h I row2-row1	1.01328	1
Var 36h NI row2-row1	0.88429	0.549
Var 60h I row2-row1	1.21555	0.562
Var 60h NI row2-row1	1.16333	0.904
Time course 0hI-0hNI	1.17355	0.719
Time course 12hI-12hNI	1.02456	0.849
Time course 36hI-36hNI	0.96402	0.255
Time course 60hI-60hNI	1.12564	0.16

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	4.67303	0.248
transgenic ySAMdc/azygous control (red)	1.94241	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00536	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0949	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.22688	0.123
Manapal/WT (red)	0.73946	0.184