Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.19.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99256	0.858
27DAP/17DAP	1.28817	0.708
39DAP/27DAP	1.05685	0.782
41DAP/39DAP	0.9312	0.743
42DAP/41DAP	1.00573	1
43DAP/42DAP	0.90158	0.815
47DAP/43DAP	1.2047	0.241
52DAP/47DAP	0.77777	0.554
57DAP/52DAP	1.17199	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98943	0.645
17DAP/reference	0.82269	0.014
27DAP/reference	0.94995	0.525
39DAP/reference	0.98672	0.816
41DAP/reference	0.82953	0.065
42DAP/reference	0.96427	0.134
43DAP/reference	0.87693	0.058
47DAP/reference	1.11124	0.081
52DAP/reference	1.11957	0.476
57DAP/reference	1.07457	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3776	0.036
27DAP/17DAP	0.77988	0.614
39DAP/27DAP	1.20323	0.471
41DAP/39DAP	0.86721	0.512
42DAP/41DAP	1.0906	0.753
43DAP/42DAP	1.01601	1
47DAP/43DAP	0.9561	0.815
52DAP/47DAP	1.16392	0.524
57DAP/52DAP	0.97837	0.763
57DAP/7DAP	1.2007

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00425	1
17DAP/reference	0.9147	0.192
27DAP/reference	0.91404	0.215
39DAP/reference	0.85725	0.109
41DAP/reference	0.74349	0.016
42DAP/reference	0.889	0.123
43DAP/reference	0.88766	0.061
47DAP/reference	1.09183	0.595
52DAP/reference	0.75259	0.061
57DAP/reference	0.9049	0.128

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97714	0.72
17DAP/reference	1.10929	0.161
27DAP/reference	1.08328	0.692
39DAP/reference	1.14406	0.17
41DAP/reference	1.19782	0.502
42DAP/reference	1.08903	0.81
43DAP/reference	0.98186	0.633
47DAP/reference	0.90783	0.133
52DAP/reference	0.99513	0.666
57DAP/reference	0.99782	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06373	0.758
17DAP/reference	0.90522	0.143
27DAP/reference	0.933	0.184
39DAP/reference	0.97659	0.504
41DAP/reference	0.78591	0.025
42DAP/reference	0.97807	0.671
43DAP/reference	1.01482	0.738
47DAP/reference	0.92615	0.224
52DAP/reference	1.14313	0.854
57DAP/reference	1.22255	0.285

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85587	1
26DAP/20DAP	1.01581	1
34DAP/26DAP	0.95313	0.917
51DAP/34DAP	2.605	0.613
52DAP/51DAP	0.99843	1
53DAP/52DAP	0.99209	0.938
55DAP/53DAP	0.81023	0.5
57DAP/55DAP	1.02124	1
62DAP/57DAP	0.91569	0.466
68DAP/62DAP	1.13493	0.754
68DAP/14DAP	1.31249	0.279

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.58606	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.75018	0.232
Mature Green Tomato/Ripe Tomato	0.73761	0.107
Immature Eggplant/Mature Eggplant	1.25778	0.417
Ripe Pepper/Ripe Tomato	0.83059	1
Mature Eggplant/Ripe Tomato	0.48325	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91004
1-1-2/M82	1.09928	0.977
12-2/M82	0.87919
12-4/M82	0.81555	0.358
1-3/M82	2.0709
2-1-1/M82	8.54621	0.689
2-1/M82	1.42106
2-6/M82	1.33972	0.695
3-2/M82	1.25724	0.549
4-1-1/M82	1.19894	1
4-1/M82	N/A	N/A
4-3-2/M82	1.43065
4-3/M82	1.71608	0.268
5-3/M82	0.93102	1
6-2/M82	0.9227	1
6-3/M82	0.86851	1
7-1/M82	1.38427
7-2/M82	1.00924	1
9-3-2/M82	1.30204	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.34523	0.277
IL2-6/WTpooled	0.94088	0.383
IL7-5/WTpooled	1.28822	0.75
IL7-3/WTpooled	1.25211	1
IL12-4/WTpooled	1.10805	0.42
IL1-4/WTpooled	0.92852	0.834
WT/WTpooled	1.02813	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	0.93099	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.71827	1
DC3000/delta hrp 6h	0.88246	0.95
DC3000/delta hrp 12h	1.03968	1
DC3000/delta hrp 24h	1.24468	0.047

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	0.90842	0.826

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03399	1
Exp 36h	0.67221	0.406
Exp 60h	0.74269	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02527	1
Var 0h	0.88927	1
Var 12h I row2-row1	1.12705	0.196
Var 12h NI row2-row1	1.13837
Var 36h I row2-row1	1.08445	0.304
Var 36h NI row2-row1	0.76324	0.706
Var 60h I row2-row1	0.88959	0.582
Var 60h NI row2-row1	0.9035	1
Time course 0hI-0hNI	1.18117	0.603
Time course 12hI-12hNI	1.00425	1
Time course 36hI-36hNI	1.21432	0.009
Time course 60hI-60hNI	1.49768	0.019

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)	1.06546	0.3
transgenic ySAMdc/azygous control (breaker)	1.40594	0.166
transgenic ySAMdc/azygous control (red)	1.01115	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99023	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.32847	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.74848	0.083
Manapal/WT (break)	1.20389	0.381
Manapal/WT (red)	0.97779	0.863