Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87343	0.464
27DAP/17DAP	1.43815	0.877
39DAP/27DAP	0.82564	0.449
41DAP/39DAP	1.39411	0.185
42DAP/41DAP	1.80972	0.081
43DAP/42DAP	1.26013	0.982
47DAP/43DAP	1.26771	0.542
52DAP/47DAP	1.12983	0.902
57DAP/52DAP	1.15825	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96233	0.465
17DAP/reference	1.15667	0.04
27DAP/reference	1.16059	0.043
39DAP/reference	1.15749	0.108
41DAP/reference	1.02614	0.855
42DAP/reference	1.02485	1
43DAP/reference	1.1031	0.175
47DAP/reference	0.99546	0.636
52DAP/reference	0.91799	0.195
57DAP/reference	0.91572	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31151	0.547
27DAP/17DAP	1.10312	0.842
39DAP/27DAP	1.41593	0.143
41DAP/39DAP	0.5652	0.016
42DAP/41DAP	1.67889	0.019
43DAP/42DAP	3.38445	0.014
47DAP/43DAP	0.95983	0.855
52DAP/47DAP	1.17927	0.598
57DAP/52DAP	1.00014	0.833
57DAP/7DAP	1.69668	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03032	0.691
17DAP/reference	1.04156	0.244
27DAP/reference	0.93189	0.071
39DAP/reference	0.94849	0.17
41DAP/reference	1.01391	0.864
42DAP/reference	0.95672	0.13
43DAP/reference	0.96017	0.241
47DAP/reference	0.953	0.293
52DAP/reference	0.92631	0.072
57DAP/reference	0.99635	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96029	0.548
17DAP/reference	0.99103	0.673
27DAP/reference	0.91697	0.282
39DAP/reference	0.92533	0.33
41DAP/reference	0.92761	0.268
42DAP/reference	0.82711	0.012
43DAP/reference	1.14233	0.547
47DAP/reference	0.96654	0.39
52DAP/reference	0.9323	0.28
57DAP/reference	1.0365	0.724

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02676	0.505
17DAP/reference	0.96687	0.56
27DAP/reference	0.95847	0.286
39DAP/reference	1.03778	0.365
41DAP/reference	0.96733	0.331
42DAP/reference	0.99581	0.816
43DAP/reference	0.92728	0.197
47DAP/reference	1.25109	0.07
52DAP/reference	1.03702	0.826
57DAP/reference	0.85586	0.062

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18836	0.966
26DAP/20DAP	0.50355	0.512
34DAP/26DAP	1.54012	1
51DAP/34DAP	1.07184	0.96
52DAP/51DAP	0.61382	1
53DAP/52DAP	1.03801	0.978
55DAP/53DAP	0.96343	0.775
57DAP/55DAP	1.29417	0.87
62DAP/57DAP	1.44291	0.622
68DAP/62DAP	0.85715	0.668
68DAP/14DAP	0.55038	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.21403	0.029

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.05038	1
Mature Green Tomato/Ripe Tomato	0.15986	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.65532	0.224
Mature Eggplant/Ripe Tomato	0.03793	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.41211	0.742
1-1-2/M82	N/A	N/A
12-2/M82	1.05437	1
12-4/M82	1.12464	1
1-3/M82	1.53527	1
2-1-1/M82	1.289	0.764
2-1/M82	1.26489	1
2-6/M82	0.82566	1
3-2/M82	N/A	N/A
4-1-1/M82	0.92085	1
4-1/M82	1.0635	0.512
4-3-2/M82	0.51466
4-3/M82	1.56918	0.268
5-3/M82	0.87716	1
6-2/M82	1.00674	1
6-3/M82	0.95845	1
7-1/M82	N/A	N/A
7-2/M82	0.74228
9-3-2/M82	0.98664	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97345	1
IL2-6/WTpooled	1.03741	0.659
IL7-5/WTpooled	0.77957	1
IL7-3/WTpooled	1.07256	1
IL12-4/WTpooled	0.82587	0.71
IL1-4/WTpooled	0.70958
WT/WTpooled	0.93372	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	0.68967	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96711	1
DC3000/delta hrp 6h	0.73669
DC3000/delta hrp 12h	0.98387	1
DC3000/delta hrp 24h	0.87226	0.346

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	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	0.98515
Var 0h	0.89092	1
Var 12h I row2-row1	1.00636	0.544
Var 12h NI row2-row1	0.98551	0.906
Var 36h I row2-row1	2.37622	1
Var 36h NI row2-row1	1.06921	0.852
Var 60h I row2-row1	1.11553	1
Var 60h NI row2-row1	0.97193	0.904
Time course 0hI-0hNI	0.95958	0.799
Time course 12hI-12hNI	0.88985	0.111
Time course 36hI-36hNI	0.63903	0.023
Time course 60hI-60hNI	0.32179	0.011

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)	1.02738	0.921
transgenic ySAMdc/azygous control (breaker)	0.95438	1
transgenic ySAMdc/azygous control (red)	1.12226	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.992	0.609

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06138	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.11313	0.087
Manapal/WT (break)	0.98966	1
Manapal/WT (red)	0.90127	0.181