Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.16.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93293	0.61
27DAP/17DAP	1.17457	0.881
39DAP/27DAP	1.23086	0.885
41DAP/39DAP	0.83399	0.37
42DAP/41DAP	1.16434	0.888
43DAP/42DAP	1.05201	1
47DAP/43DAP	1.10515	0.793
52DAP/47DAP	1.157	0.96
57DAP/52DAP	1.1665	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96714	0.476
17DAP/reference	1.05678	0.546
27DAP/reference	1.03803	0.75
39DAP/reference	1.03284	0.889
41DAP/reference	0.88755	0.154
42DAP/reference	0.95623	0.095
43DAP/reference	1.08937	0.34
47DAP/reference	0.92148	0.071
52DAP/reference	0.92872	0.195
57DAP/reference	0.88444	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77238	0.03
27DAP/17DAP	1.03325	0.924
39DAP/27DAP	1.14635	0.691
41DAP/39DAP	0.9888	0.997
42DAP/41DAP	1.02473	1
43DAP/42DAP	0.97954	0.801
47DAP/43DAP	0.91428	0.418
52DAP/47DAP	0.79218	0.109
57DAP/52DAP	0.98267	0.716
57DAP/7DAP	0.74449	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8204	0.062
17DAP/reference	0.77451	0.021
27DAP/reference	0.79283	0.01
39DAP/reference	0.85564	0.011
41DAP/reference	0.82399	0.024
42DAP/reference	0.82185	0.01
43DAP/reference	0.848	0.014
47DAP/reference	0.86095	0.101
52DAP/reference	0.82185	0.023
57DAP/reference	0.85983	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77587	0.048
17DAP/reference	0.8047	0.027
27DAP/reference	0.91356	0.257
39DAP/reference	0.87764	0.202
41DAP/reference	0.94808	0.284
42DAP/reference	0.82705	0.037
43DAP/reference	0.76882	0.027
47DAP/reference	0.93498	0.178
52DAP/reference	0.81831	0.011
57DAP/reference	0.7558	0.023

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76108	0.038
17DAP/reference	0.87316	0.198
27DAP/reference	0.83069	0.042
39DAP/reference	0.809	0.018
41DAP/reference	0.91888	0.07
42DAP/reference	1.03299	0.877
43DAP/reference	0.9621	0.432
47DAP/reference	1.01644	0.754
52DAP/reference	1.12456	0.614
57DAP/reference	0.89511	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23932	1
26DAP/20DAP	1.22469	0.374
34DAP/26DAP	0.86807	0.848
51DAP/34DAP	1.19094
52DAP/51DAP	0.86972	1
53DAP/52DAP	0.85516	0.527
55DAP/53DAP	0.85868	0.462
57DAP/55DAP	1.60026	0.474
62DAP/57DAP	0.93214	0.681
68DAP/62DAP	1.05111	0.956
68DAP/14DAP	1.06622	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.30209	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40711	0.089
Mature Green Tomato/Ripe Tomato	1.06998	0.69
Immature Eggplant/Mature Eggplant	0.78864	0.176
Ripe Pepper/Ripe Tomato	0.98319	1
Mature Eggplant/Ripe Tomato	0.95937	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.93419
12-2/M82	N/A	N/A
12-4/M82	1.08114	1
1-3/M82	N/A	N/A
2-1-1/M82	0.69906
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.25824
4-3/M82	1.86998	0.268
5-3/M82	1.11348	1
6-2/M82	N/A	N/A
6-3/M82	0.96173
7-1/M82	0.7242
7-2/M82	0.99386
9-3-2/M82	1.05389	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94468	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.11382	1
IL12-4/WTpooled	0.96339	1
IL1-4/WTpooled	0.6519
WT/WTpooled	1.03148	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	1.43916	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.20471	0.823
DC3000/delta hrp 6h	1.00252	0.95
DC3000/delta hrp 12h	0.95703	1
DC3000/delta hrp 24h	1.03736	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.28937	0.145
DC3000 delta B/DC3000 delta AB	1.36216	0.137

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91023	1
Exp 36h	1.05427	1
Exp 60h	1.12647	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07752	1
Var 0h	1.26244	0.374
Var 12h I row2-row1	0.84535	0.39
Var 12h NI row2-row1	1.05302	1
Var 36h I row2-row1	1.218	0.41
Var 36h NI row2-row1	0.97941	0.791
Var 60h I row2-row1	0.73581	0.439
Var 60h NI row2-row1	0.82426	0.483
Time course 0hI-0hNI	1.21207	0.486
Time course 12hI-12hNI	1.04451	0.773
Time course 36hI-36hNI	1.08218	0.799
Time course 60hI-60hNI	1.59878	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)	1.07278	0.235
transgenic ySAMdc/azygous control (breaker)	0.76843	0.173
transgenic ySAMdc/azygous control (red)	0.98179	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07577	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73911	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79735	0.172
Manapal/WT (break)	0.99014	1
Manapal/WT (red)	1.17284	0.413