Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99593	0.901
27DAP/17DAP	0.94104	0.898
39DAP/27DAP	0.97677	0.733
41DAP/39DAP	0.90887	0.582
42DAP/41DAP	1.34529	0.544
43DAP/42DAP	1.59466	0.224
47DAP/43DAP	0.94485	0.794
52DAP/47DAP	0.97751	0.92
57DAP/52DAP	0.99907	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67724	0.026
17DAP/reference	0.76574	0.009
27DAP/reference	0.89445	0.137
39DAP/reference	0.87242	0.164
41DAP/reference	0.75242	0.012
42DAP/reference	1.10971	0.009
43DAP/reference	0.98147	0.675
47DAP/reference	1.04728	0.558
52DAP/reference	0.88826	0.237
57DAP/reference	1.11703	0.057

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07114	0.881
27DAP/17DAP	0.91726	0.748
39DAP/27DAP	1.04355	0.691
41DAP/39DAP	1.06322	0.868
42DAP/41DAP	0.88787	0.267
43DAP/42DAP	1.15503	0.324
47DAP/43DAP	1.04736	0.833
52DAP/47DAP	0.87721	0.645
57DAP/52DAP	0.84218	0.441
57DAP/7DAP	1.32348	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19472	0.351
17DAP/reference	1.63226	0.012
27DAP/reference	1.32474	0.06
39DAP/reference	1.30876	0.297
41DAP/reference	1.23809	0.159
42DAP/reference	1.34261	0.405
43DAP/reference	1.40354	0.008
47DAP/reference	1.98664	0.042
52DAP/reference	1.14367	0.266
57DAP/reference	1.189	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70648	0.046
17DAP/reference	0.72552	0.013
27DAP/reference	0.98739	0.598
39DAP/reference	1.18075	0.136
41DAP/reference	1.04261	0.862
42DAP/reference	1.03457	0.744
43DAP/reference	0.83629	0.166
47DAP/reference	1.06478	0.264
52DAP/reference	1.03686	0.322
57DAP/reference	0.84274	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54718	0.356
17DAP/reference	1.12985	0.72
27DAP/reference	1.79182	0.081
39DAP/reference	1.34509	0.116
41DAP/reference	1.27975	0.052
42DAP/reference	1.62579	0.023
43DAP/reference	1.18863	0.209
47DAP/reference	1.20993	0.085
52DAP/reference	1.45764	0.048
57DAP/reference	1.40783	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97827	1
26DAP/20DAP	1.1146	0.7
34DAP/26DAP	0.90151	0.627
51DAP/34DAP	0.95517	0.791
52DAP/51DAP	0.86296	1
53DAP/52DAP	1.19821	0.537
55DAP/53DAP	0.95529	0.838
57DAP/55DAP	1.04191	1
62DAP/57DAP	0.92704	0.871
68DAP/62DAP	1.52603	0.034
68DAP/14DAP	1.62323	0.279

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.54561	0.029

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.49304	0.058
Mature Green Tomato/Ripe Tomato	2.67173	0.017
Immature Eggplant/Mature Eggplant	0.60451	0.065
Ripe Pepper/Ripe Tomato	5.23891	0.258
Mature Eggplant/Ripe Tomato	4.10991	0.268

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	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.36509
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40767	0.277
IL2-6/WTpooled	0.65497	0.337
IL7-5/WTpooled	1.11899	0.792
IL7-3/WTpooled	1.38747	0.362
IL12-4/WTpooled	1.09742	0.737
IL1-4/WTpooled	0.95197	0.834
WT/WTpooled	0.98397	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	1.07981	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84899	0.839
DC3000/delta hrp 6h	1.01262	1
DC3000/delta hrp 12h	0.95972	1
DC3000/delta hrp 24h	0.2901	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54371	0.025
DC3000 delta B/DC3000 delta AB	0.72981	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15152	1
Exp 36h	1.01575	1
Exp 60h	0.99537	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89051	1
Var 0h	1.0232	1
Var 12h I row2-row1	0.89611	0.705
Var 12h NI row2-row1	1.11745	0.649
Var 36h I row2-row1	1.21072	1
Var 36h NI row2-row1	1.38381	1
Var 60h I row2-row1	0.82817
Var 60h NI row2-row1	0.99746	1
Time course 0hI-0hNI	0.95497	0.615
Time course 12hI-12hNI	0.92532	0.347
Time course 36hI-36hNI	0.77827	0.023
Time course 60hI-60hNI	0.25567	0.005

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)	0.89375	0.348
transgenic ySAMdc/azygous control (breaker)	0.62917	0.119
transgenic ySAMdc/azygous control (red)	1.09917	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13234	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9985	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.44355	0.096
Manapal/WT (break)	1.10559	1
Manapal/WT (red)	1.03703	1