Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20174	0.878
27DAP/17DAP	1.11721	0.872
39DAP/27DAP	1.31058	0.335
41DAP/39DAP	0.90005	0.579
42DAP/41DAP	1.04266	0.941
43DAP/42DAP	0.99505	0.937
47DAP/43DAP	1.16989	0.459
52DAP/47DAP	0.85601	0.617
57DAP/52DAP	1.02182	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00126	0.707
17DAP/reference	1.15171	0.02
27DAP/reference	1.04756	0.863
39DAP/reference	1.27711	0.122
41DAP/reference	1.4025	0.014
42DAP/reference	0.92211	0.075
43DAP/reference	1.02703	0.425
47DAP/reference	0.90647	0.071
52DAP/reference	0.84392	0.125
57DAP/reference	0.87065	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83734	0.105
27DAP/17DAP	1.07176	0.909
39DAP/27DAP	1.05948	0.587
41DAP/39DAP	1.04775	1
42DAP/41DAP	1.01456	0.884
43DAP/42DAP	1.13498	0.324
47DAP/43DAP	0.94937	0.781
52DAP/47DAP	1.07585	0.696
57DAP/52DAP	0.72987	0.106
57DAP/7DAP	0.95871	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84608	0.115
17DAP/reference	0.79344	0.016
27DAP/reference	0.84915	0.035
39DAP/reference	0.79393	0.011
41DAP/reference	0.93199	0.203
42DAP/reference	0.90768	0.073
43DAP/reference	0.81917	0.014
47DAP/reference	0.72306	0.036
52DAP/reference	0.83121	0.077
57DAP/reference	0.87604	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07507	0.687
17DAP/reference	1.1712	0.191
27DAP/reference	1.13953	0.316
39DAP/reference	0.86698	0.113
41DAP/reference	0.95114	0.384
42DAP/reference	1.21088	0.226
43DAP/reference	1.76907	0.028
47DAP/reference	1.32447	0.033
52DAP/reference	0.92179	0.203
57DAP/reference	1.04525	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91711	0.311
17DAP/reference	1.02185	0.977
27DAP/reference	0.90071	0.257
39DAP/reference	0.95939	0.43
41DAP/reference	0.97249	0.56
42DAP/reference	0.84153	0.172
43DAP/reference	0.90749	0.033
47DAP/reference	1.01714	1
52DAP/reference	0.86507	0.262
57DAP/reference	0.7542	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1252	0.966
26DAP/20DAP	0.86348	0.512
34DAP/26DAP	1.15107	0.819
51DAP/34DAP	0.83112	0.19
52DAP/51DAP	1.10609	0.42
53DAP/52DAP	1.19804	0.284
55DAP/53DAP	1.07852	0.869
57DAP/55DAP	1.35765	0.34
62DAP/57DAP	1.07918	1
68DAP/62DAP	0.94873	0.579
68DAP/14DAP	0.58341	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68293	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02545	0.835
Immature Eggplant/Mature Eggplant	35.9156	0.063
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	7.62403

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00563	1
1-1-2/M82	1.18438	1
12-2/M82	1.222	1
12-4/M82	1.3819	0.563
1-3/M82	0.89356	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.02056	1
3-2/M82	0.94789	1
4-1-1/M82	0.94555	1
4-1/M82	1.53665	0.466
4-3-2/M82	1.03739	1
4-3/M82	N/A	N/A
5-3/M82	0.97517	1
6-2/M82	0.72714
6-3/M82	1.11483	1
7-1/M82	0.94389
7-2/M82	0.72282	0.578
9-3-2/M82	1.01181	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7187	0.247
IL2-6/WTpooled	1.14209	0.531
IL7-5/WTpooled	1.31157	0.792
IL7-3/WTpooled	0.77591	0.31
IL12-4/WTpooled	0.92474	1
IL1-4/WTpooled	0.773	0.834
WT/WTpooled	1.09689	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	2.45255	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19968	0.547
DC3000/delta hrp 6h	1.8203	1
DC3000/delta hrp 12h	1.11214	1
DC3000/delta hrp 24h	1.59873	0.516

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	1.14133

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.59683	0.661
Exp 60h	0.49626	0.196

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05035	1
Var 0h	1.07213	0.936
Var 12h I row2-row1	1.1748	0.204
Var 12h NI row2-row1	0.98795	0.82
Var 36h I row2-row1	1.60363	1
Var 36h NI row2-row1	0.74251	0.645
Var 60h I row2-row1	0.96242	0.439
Var 60h NI row2-row1	0.97654	1
Time course 0hI-0hNI	0.96497	0.781
Time course 12hI-12hNI	0.93357	0.337
Time course 36hI-36hNI	0.9607	0.418
Time course 60hI-60hNI	3.19533	0.187

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)	1.32441	0.662
transgenic ySAMdc/azygous control (breaker)	2.98522	1
transgenic ySAMdc/azygous control (red)	0.94402	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09823	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.36195	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.61137	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.728	0.181