Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.10.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.19641	0.124
27DAP/17DAP	1.45399	0.613
39DAP/27DAP	1.01707	0.899
41DAP/39DAP	0.98281	0.841
42DAP/41DAP	0.85642	1
43DAP/42DAP	0.91345	0.851
47DAP/43DAP	1.15466	0.727
52DAP/47DAP	1.46593	0.403
57DAP/52DAP	1.20504	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89369	0.188
17DAP/reference	0.77622	0.008
27DAP/reference	1.09895	0.709
39DAP/reference	0.91347	0.121
41DAP/reference	0.64677	0.013
42DAP/reference	0.9048	0.05
43DAP/reference	0.9814	0.708
47DAP/reference	1.15224	0.154
52DAP/reference	1.17541	0.149
57DAP/reference	1.56612	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3615	0.34
27DAP/17DAP	0.86702	0.475
39DAP/27DAP	1.32786	0.128
41DAP/39DAP	0.87324	0.481
42DAP/41DAP	1.15532	0.622
43DAP/42DAP	1.07641	0.351
47DAP/43DAP	0.94978	0.597
52DAP/47DAP	1.00718	0.959
57DAP/52DAP	1.14301	0.479
57DAP/7DAP	1.5793	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00656	1
17DAP/reference	1.21467	0.019
27DAP/reference	1.30367	0.026
39DAP/reference	1.26344	0.351
41DAP/reference	1.10849	0.745
42DAP/reference	1.38898	0.076
43DAP/reference	1.11939	0.386
47DAP/reference	0.94778	0.504
52DAP/reference	0.98027	0.523
57DAP/reference	1.16591	0.035

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93106	0.441
17DAP/reference	0.92068	0.326
27DAP/reference	0.60946	0.053
39DAP/reference	0.84507	0.126
41DAP/reference	0.76347	0.03
42DAP/reference	0.71374	0.024
43DAP/reference	0.6932	0.044
47DAP/reference	1.08125	0.512
52DAP/reference	0.77286	0.025
57DAP/reference	0.97784	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18596	0.23
17DAP/reference	0.95113	0.537
27DAP/reference	1.33741	0.033
39DAP/reference	1.14569	0.406
41DAP/reference	0.96492	0.512
42DAP/reference	1.11251	0.4
43DAP/reference	0.97551	0.568
47DAP/reference	0.86258	0.139
52DAP/reference	1.79924	0.123
57DAP/reference	1.07923	0.539

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90626	0.997
26DAP/20DAP	2.01228	0.141
34DAP/26DAP	1.31762	0.819
51DAP/34DAP	1.35505	0.365
52DAP/51DAP	1.02371	1
53DAP/52DAP	0.89429	0.527
55DAP/53DAP	0.91763	0.698
57DAP/55DAP	1.0746	1
62DAP/57DAP	1.06817	1
68DAP/62DAP	1.06488	0.885
68DAP/14DAP	0.72756	0.069

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.93707	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.15885	0.176
Mature Green Tomato/Ripe Tomato	0.95755	0.522
Immature Eggplant/Mature Eggplant	0.99197	1
Ripe Pepper/Ripe Tomato	0.61417	0.224
Mature Eggplant/Ripe Tomato	0.72447	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.76807	0.616
1-1-2/M82	1.00054	1
12-2/M82	0.82483	0.678
12-4/M82	0.7328	0.358
1-3/M82	1.87042	0.248
2-1-1/M82	0.45662	N/A
2-1/M82	1.01217	N/A
2-6/M82	0.65488	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.91106	1
4-1/M82	1.16163	N/A
4-3-2/M82	0.74884	N/A
4-3/M82	0.55168	0.404
5-3/M82	1.32011	1
6-2/M82	0.77916	0.473
6-3/M82	2.06165	N/A
7-1/M82	N/A	N/A
7-2/M82	0.98347	1
9-3-2/M82	0.83736	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88991	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.49967	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.13416	0.426
WT/WTpooled	1.00025	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	1.10445	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09623	0.724
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.90088	1
DC3000/delta hrp 24h	0.63726	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.32696	0.408
DC3000 delta B/DC3000 delta AB	1.24008	0.298

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20249	1
Exp 36h	1.09273	0.489
Exp 60h	0.91674	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94048	1
Var 0h	0.92561	1
Var 12h I row2-row1	1.20924	0.544
Var 12h NI row2-row1	1.19365	0.34
Var 36h I row2-row1	1.09665	0.742
Var 36h NI row2-row1	0.74678	0.341
Var 60h I row2-row1	0.71571	0.582
Var 60h NI row2-row1	1.04772	1
Time course 0hI-0hNI	1.02731	0.867
Time course 12hI-12hNI	0.97846	0.855
Time course 36hI-36hNI	1.29692	0.011
Time course 60hI-60hNI	1.10038	0.359

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)	0.85947	0.32
transgenic ySAMdc/azygous control (breaker)	1.30258	0.178
transgenic ySAMdc/azygous control (red)	1.12345	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12353	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96379	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86723	1
Manapal/WT (break)	0.72935	0.333
Manapal/WT (red)	1.45682	0.134