Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0665	0.878
27DAP/17DAP	0.91512	0.885
39DAP/27DAP	1.15765	0.681
41DAP/39DAP	0.89319	0.607
42DAP/41DAP	0.73128	0.774
43DAP/42DAP	1.09852	1
47DAP/43DAP	1.14459	0.609
52DAP/47DAP	1.29745	0.597
57DAP/52DAP	1.07402	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95153	0.402
17DAP/reference	0.88228	0.031
27DAP/reference	1.00893	1
39DAP/reference	0.88902	0.081
41DAP/reference	0.92271	0.201
42DAP/reference	0.90715	0.02
43DAP/reference	1.06724	0.73
47DAP/reference	0.92992	0.242
52DAP/reference	1.07779	0.128
57DAP/reference	1.27627	0.026

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99618	0.847
27DAP/17DAP	1.22072	0.518
39DAP/27DAP	1.13215	0.654
41DAP/39DAP	1.30883	0.579
42DAP/41DAP	0.855	0.279
43DAP/42DAP	0.87437	0.293
47DAP/43DAP	1.12695	0.674
52DAP/47DAP	1.14767	0.635
57DAP/52DAP	0.96094	0.709
57DAP/7DAP	1.20158	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98066	0.613
17DAP/reference	0.96791	0.447
27DAP/reference	0.79863	0.066
39DAP/reference	1.08555	0.74
41DAP/reference	0.96174	0.489
42DAP/reference	0.88491	0.169
43DAP/reference	0.90443	0.22
47DAP/reference	1.34938	0.093
52DAP/reference	1.09684	0.832
57DAP/reference	1.08871	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81857	0.049
17DAP/reference	0.79156	0.046
27DAP/reference	0.91696	0.167
39DAP/reference	0.98615	0.469
41DAP/reference	1.13152	0.406
42DAP/reference	0.8822	0.016
43DAP/reference	0.82551	0.102
47DAP/reference	0.89515	0.068
52DAP/reference	1.01	1
57DAP/reference	0.76592	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2693	0.09
17DAP/reference	0.80713	0.154
27DAP/reference	1.09866	0.721
39DAP/reference	1.08366	0.512
41DAP/reference	0.90735	0.56
42DAP/reference	1.10235	0.556
43DAP/reference	1.06661	0.547
47DAP/reference	1.03517	1
52DAP/reference	1.02683	0.979
57DAP/reference	1.27936	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.258	0.966
26DAP/20DAP	1.18225	0.615
34DAP/26DAP	1.40996	1
51DAP/34DAP	1.12997	0.917
52DAP/51DAP	0.98014	1
53DAP/52DAP	1.34769	0.334
55DAP/53DAP	1.04713	0.908
57DAP/55DAP	0.94222	0.821
62DAP/57DAP	0.81004	0.681
68DAP/62DAP	1.7592	0.155
68DAP/14DAP	1.90144	0.103

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81794	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.75087	0.363
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.12306	1
Mature Eggplant/Ripe Tomato	0.76223	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.95979	1
12-2/M82	0.8891
12-4/M82	0.80826	0.619
1-3/M82	1.55641	0.479
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.21298	0.695
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	1.16531	1
5-3/M82	1.30673	0.496
6-2/M82	0.73842
6-3/M82	N/A	N/A
7-1/M82	0.86891
7-2/M82	1.05813
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12491	0.277
IL2-6/WTpooled	1.00749	1
IL7-5/WTpooled	1.23984	0.792
IL7-3/WTpooled	1.07103	1
IL12-4/WTpooled	1.01136	1
IL1-4/WTpooled	1.10667	1
WT/WTpooled	0.9392	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	0.94995	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97095	1
DC3000/delta hrp 6h	0.6876	0.95
DC3000/delta hrp 12h	1.0155	1
DC3000/delta hrp 24h	0.45153	0.034

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	N/A	N/A
Exp 36h	1.18284	0.326
Exp 60h	1.02665	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.97494	1
Var 12h I row2-row1	0.90587	0.467
Var 12h NI row2-row1	4.50991
Var 36h I row2-row1	0.70561
Var 36h NI row2-row1	1.09111	0.482
Var 60h I row2-row1	1.33578
Var 60h NI row2-row1	0.65885	1
Time course 0hI-0hNI	1.00337	1
Time course 12hI-12hNI	0.94095	0.511
Time course 36hI-36hNI	1.21484	0.08
Time course 60hI-60hNI	0.9889	1

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)	1.05354	0.305
transgenic ySAMdc/azygous control (breaker)	1.31597	0.248
transgenic ySAMdc/azygous control (red)	1.03853	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0368	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10271	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22195	0.307
Manapal/WT (break)	1.60102	0.381
Manapal/WT (red)	1.98517	0.15