Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.8.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30841	0.291
27DAP/17DAP	1.60073	0.424
39DAP/27DAP	1.26843	0.361
41DAP/39DAP	0.98819	0.939
42DAP/41DAP	1.28064	0.556
43DAP/42DAP	1.26721	0.755
47DAP/43DAP	1.06615	0.727
52DAP/47DAP	0.94576	0.823
57DAP/52DAP	0.9341	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78537	0.032
17DAP/reference	0.88257	0.298
27DAP/reference	1.45507	0.01
39DAP/reference	1.22358	0.027
41DAP/reference	1.13515	0.421
42DAP/reference	1.24229	0.012
43DAP/reference	1.23364	0.022
47DAP/reference	1.14558	0.081
52DAP/reference	1.0395	0.912
57DAP/reference	1.28376	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.79381	0.075
27DAP/17DAP	0.74126	0.091
39DAP/27DAP	1.68226	0.099
41DAP/39DAP	0.80252	0.384
42DAP/41DAP	1.37157	0.084
43DAP/42DAP	1.02585	0.788
47DAP/43DAP	1.87759	0.906
52DAP/47DAP	1.17576	0.504
57DAP/52DAP	0.8863	0.342
57DAP/7DAP	1.4851	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83642	0.072
17DAP/reference	0.88029	0.082
27DAP/reference	0.99056	0.614
39DAP/reference	1.21572	0.014
41DAP/reference	0.92511	0.311
42DAP/reference	0.93319	0.371
43DAP/reference	1.20091	0.14
47DAP/reference	1.69468	0.014
52DAP/reference	1.15709	0.081
57DAP/reference	1.11772	0.804

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.871	0.238
17DAP/reference	0.76662	0.007
27DAP/reference	0.97634	0.483
39DAP/reference	0.96896	0.442
41DAP/reference	0.98461	0.493
42DAP/reference	0.88525	0.135
43DAP/reference	1.07577	0.713
47DAP/reference	1.04274	0.498
52DAP/reference	0.78054	0.029
57DAP/reference	1.05645	0.827

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95013	0.455
17DAP/reference	0.9448	0.55
27DAP/reference	0.90229	0.243
39DAP/reference	1.07692	0.218
41DAP/reference	1.03568	0.84
42DAP/reference	1.10447	0.481
43DAP/reference	1.23219	0.175
47DAP/reference	1.14242	0.294
52DAP/reference	1.06074	0.631
57DAP/reference	1.13968	0.378

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00062	1
26DAP/20DAP	2.30852	0.099
34DAP/26DAP	1.33759	1
51DAP/34DAP	1.34058	0.535
52DAP/51DAP	0.92336	1
53DAP/52DAP	1.90139	0.121
55DAP/53DAP	0.69062	0.075
57DAP/55DAP	0.96087	0.821
62DAP/57DAP	0.63657	0.088
68DAP/62DAP	0.89163	0.609
68DAP/14DAP	0.85459	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.57371	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.28678	0.073
Mature Green Tomato/Ripe Tomato	1.00365	1
Immature Eggplant/Mature Eggplant	29.6618	0.05
Ripe Pepper/Ripe Tomato	1.31261	0.236
Mature Eggplant/Ripe Tomato	0.40532	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.34766	0.742
1-1-2/M82	1.18765	1
12-2/M82	1.15392	1
12-4/M82	1.04937	1
1-3/M82	1.1473	1
2-1-1/M82	0.9499	1
2-1/M82	0.59214	0.322
2-6/M82	1.0656	0.695
3-2/M82	1.23624	0.967
4-1-1/M82	0.9689	1
4-1/M82	1.20437	1
4-3-2/M82	1.09633	1
4-3/M82	1.21685	1
5-3/M82	0.92268	1
6-2/M82	1.62894	1
6-3/M82	0.84219	0.857
7-1/M82	0.96287	1
7-2/M82	1.07838
9-3-2/M82	1.41481	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.92795
IL12-4/WTpooled	0.65917	1
IL1-4/WTpooled	1.033	0.426
WT/WTpooled	1.1416	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	1.18068	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13209	0.692
DC3000/delta hrp 6h	0.92604	0.95
DC3000/delta hrp 12h	1.13372	1
DC3000/delta hrp 24h	1.21624	0.308

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	1.32059

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13282	0.254
Exp 36h	0.97078	0.82
Exp 60h	1.3614	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09065	1
Var 0h	1.22035	0.311
Var 12h I row2-row1	0.97377	0.948
Var 12h NI row2-row1	0.99402	1
Var 36h I row2-row1	1.06906	1
Var 36h NI row2-row1	1.29666	1
Var 60h I row2-row1	0.84455	0.285
Var 60h NI row2-row1	1.00723	1
Time course 0hI-0hNI	1.00397	1
Time course 12hI-12hNI	0.99085	0.994
Time course 36hI-36hNI	0.99634	0.742
Time course 60hI-60hNI	2.32609	0.008

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)	0.82105	0.286
transgenic ySAMdc/azygous control (breaker)	1.67926	0.178
transgenic ySAMdc/azygous control (red)	1.1557	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12222	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.5328	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0148	1
Manapal/WT (break)	1.21339	0.14
Manapal/WT (red)	0.80273	0.181