Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.3.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08739	0.964
27DAP/17DAP	0.91566	0.819
39DAP/27DAP	1.23478	0.405
41DAP/39DAP	0.70155	0.112
42DAP/41DAP	1.0788	1
43DAP/42DAP	1.15346	1
47DAP/43DAP	0.73847	0.28
52DAP/47DAP	0.97611	0.752
57DAP/52DAP	1.63491	0.892

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16322	0.252
17DAP/reference	0.86149	0.63
27DAP/reference	0.727	0.201
39DAP/reference	0.99332	0.941
41DAP/reference	0.88302	0.667
42DAP/reference	0.99895	0.665
43DAP/reference	N/A	N/A
47DAP/reference	0.73768	0.004
52DAP/reference	1.06277
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.52572	0.038
27DAP/17DAP	1.30007	0.103
39DAP/27DAP	0.53744	0.028
41DAP/39DAP	1.43989	0.876
42DAP/41DAP	0.87746	0.387
43DAP/42DAP	0.50239	0.022
47DAP/43DAP	0.78678	0.046
52DAP/47DAP	1.12565	0.66
57DAP/52DAP	1.13511	0.598
57DAP/7DAP	1.12092	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85283	0.183
17DAP/reference	0.82382	0.013
27DAP/reference	0.78176	0.01
39DAP/reference	0.77094	0.011
41DAP/reference	0.78371	0.034
42DAP/reference	0.82002	0.028
43DAP/reference	0.69937	0.009
47DAP/reference	0.96381	0.671
52DAP/reference	0.69129	0.011
57DAP/reference	0.72181	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92006	0.655
17DAP/reference	1.53416	0.052
27DAP/reference	1.08288	0.81
39DAP/reference	1.1714	0.588
41DAP/reference	1.54821
42DAP/reference	1.38713	0.102
43DAP/reference	1.02597	0.863
47DAP/reference	1.05044	0.353
52DAP/reference	1.39877	0.007
57DAP/reference	1.6731	0.034

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80322	0.045
17DAP/reference	0.88589	0.335
27DAP/reference	0.83854	0.043
39DAP/reference	0.68685	0.012
41DAP/reference	0.83731	0.033
42DAP/reference	0.88301	0.361
43DAP/reference	0.9483	0.416
47DAP/reference	1.2016	0.501
52DAP/reference	0.85651	0.31
57DAP/reference	1.04825	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	N/A	N/A
26DAP/20DAP	1.50978	0.136
34DAP/26DAP	1.10477	1
51DAP/34DAP	1.16518	0.429
52DAP/51DAP	0.74679	0.151
53DAP/52DAP	1.94349	0.041
55DAP/53DAP	1.00863	0.917
57DAP/55DAP	1.29646	0.745
62DAP/57DAP	0.90313	0.994
68DAP/62DAP	1.27238
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.29532	0.047

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.13624	0.881
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	3.02888
Mature Eggplant/Ripe Tomato	1.5471	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.81617	0.883
1-1-2/M82	1.11545	1
12-2/M82	0.80213	0.678
12-4/M82	0.86689	0.319
1-3/M82	2.06722	0.26
2-1-1/M82	0.96629	1
2-1/M82	0.80697
2-6/M82	0.75362	1
3-2/M82	1.26694	0.549
4-1-1/M82	N/A	N/A
4-1/M82	0.94168
4-3-2/M82	1.50529
4-3/M82	1.0378	1
5-3/M82	1.03017	1
6-2/M82	1.24823	0.253
6-3/M82	0.97574	1
7-1/M82	1.2001
7-2/M82	1.39864	0.324
9-3-2/M82	1.02063

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09537	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.96156	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.98853	1
WT/WTpooled	N/A	N/A

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	0.98747	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95764	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.48124	1
DC3000/delta hrp 24h	0.89489	0.338

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.37307
DC3000 delta B/DC3000 delta AB	1.04342	0.714

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	1.00779	1
Var 0h	0.86301	1
Var 12h I row2-row1	1.01753	0.692
Var 12h NI row2-row1	1.01492	1
Var 36h I row2-row1	0.83908	1
Var 36h NI row2-row1	0.97973	0.791
Var 60h I row2-row1	1.05037	1
Var 60h NI row2-row1	1.13586	0.904
Time course 0hI-0hNI	1.08675	0.63
Time course 12hI-12hNI	1.01577	0.892
Time course 36hI-36hNI	0.88766	0.241
Time course 60hI-60hNI	1.27308	0.009

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)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.04901	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98443	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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)	1.58811	1
Manapal/WT (red)	0.87921	0.242