Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.2.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06645	0.812
27DAP/17DAP	1.36193	0.618
39DAP/27DAP	1.05784	1
41DAP/39DAP	1.12649	0.624
42DAP/41DAP	1.01117	1
43DAP/42DAP	1.11696	0.957
47DAP/43DAP	1.30925	0.223
52DAP/47DAP	1.00311	0.982
57DAP/52DAP	1.04527	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93852	0.371
17DAP/reference	1.02837	0.653
27DAP/reference	0.95906	0.567
39DAP/reference	0.97243	0.6
41DAP/reference	0.96167	0.542
42DAP/reference	0.88347	0.004
43DAP/reference	0.94447	0.448
47DAP/reference	1.08318	0.306
52DAP/reference	1.28517	0.242
57DAP/reference	1.20171	0.211

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22665	0.062
27DAP/17DAP	0.92037	0.614
39DAP/27DAP	1.11831	0.388
41DAP/39DAP	0.97503	0.968
42DAP/41DAP	1.29786	0.81
43DAP/42DAP	1.11285	0.176
47DAP/43DAP	1.05367	0.884
52DAP/47DAP	1.22862	0.428
57DAP/52DAP	1.18147	0.398
57DAP/7DAP	1.06794

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21313	0.117
17DAP/reference	1.17337	0.361
27DAP/reference	1.22306	0.131
39DAP/reference	1.37357	0.017
41DAP/reference	1.48707	0.012
42DAP/reference	1.5669	0.007
43DAP/reference	1.49537	0.02
47DAP/reference	1.0887	0.525
52DAP/reference	1.29057	0.041
57DAP/reference	1.2794	0.049

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93752	0.441
17DAP/reference	0.92048	0.077
27DAP/reference	0.86277	0.123
39DAP/reference	0.99785	0.661
41DAP/reference	0.92753	0.291
42DAP/reference	1.00365	1
43DAP/reference	0.86966	0.181
47DAP/reference	0.92916	0.178
52DAP/reference	0.9434	0.28
57DAP/reference	0.9572	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18131	0.134
17DAP/reference	1.15926	0.371
27DAP/reference	1.38032	0.022
39DAP/reference	1.26459	0.026
41DAP/reference	1.49967	0.031
42DAP/reference	1.2936	0.124
43DAP/reference	1.22393	0.439
47DAP/reference	1.10512	0.372
52DAP/reference	1.14087	0.262
57DAP/reference	1.16245	0.298

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98687	1
26DAP/20DAP	0.97574	1
34DAP/26DAP	1.01095	1
51DAP/34DAP	1.11504	0.677
52DAP/51DAP	0.89555	1
53DAP/52DAP	0.9477	0.835
55DAP/53DAP	1.0666	0.989
57DAP/55DAP	0.95846	0.851
62DAP/57DAP	1.85283
68DAP/62DAP	0.9968	0.914
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.33286	0.113

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68899
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.04307

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.25518
1-3/M82	0.83524	0.33
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.19782	0.405
3-2/M82	N/A	N/A
4-1-1/M82	0.7451
4-1/M82	1.23385	0.512
4-3-2/M82	1.22932	0.241
4-3/M82	N/A	N/A
5-3/M82	0.87156	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.15485
7-2/M82	N/A	N/A
9-3-2/M82	1.21023	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.81518	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07846	1
IL12-4/WTpooled	0.78449	0.554
IL1-4/WTpooled	0.92607
WT/WTpooled	0.99542	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	1.07961	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0382	0.921
DC3000/delta hrp 6h	0.78223	0.95
DC3000/delta hrp 12h	1.08427	1
DC3000/delta hrp 24h	0.94594	0.67

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	2.0191	0.19

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84965	1
Exp 36h	0.81466	0.661
Exp 60h	0.63488	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96343	1
Var 0h	2.07969	1
Var 12h I row2-row1	0.99682	1
Var 12h NI row2-row1	1.03351	1
Var 36h I row2-row1	0.96903	1
Var 36h NI row2-row1	1.11722	1
Var 60h I row2-row1	0.95131	0.952
Var 60h NI row2-row1	0.96422	0.818
Time course 0hI-0hNI	0.95415	0.582
Time course 12hI-12hNI	0.91152	0.562
Time course 36hI-36hNI	1.01107	1
Time course 60hI-60hNI	0.92597	0.319

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)	0.95314	0.289
transgenic ySAMdc/azygous control (breaker)	1.10532	0.248
transgenic ySAMdc/azygous control (red)	1.03415	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07655	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7915	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.56881	0.172
Manapal/WT (break)	1.07571	0.381
Manapal/WT (red)	1.1516	1