Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.3.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03406	0.947
27DAP/17DAP	1.06425	0.881
39DAP/27DAP	1.03011	1
41DAP/39DAP	1.17864	0.416
42DAP/41DAP	1.24498	0.899
43DAP/42DAP	1.10591	1
47DAP/43DAP	0.8969	0.652
52DAP/47DAP	1.33333	0.418
57DAP/52DAP	0.99507	0.978

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80149	0.049
17DAP/reference	0.98214	0.737
27DAP/reference	1.069	0.648
39DAP/reference	1.11214	0.079
41DAP/reference	0.99591	1
42DAP/reference	1.62751	0.014
43DAP/reference	0.93382	0.611
47DAP/reference	2.8227	0.002
52DAP/reference	1.11324	0.878
57DAP/reference	0.93195

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9767	0.732
27DAP/17DAP	1.18637	0.133
39DAP/27DAP	0.96404	0.759
41DAP/39DAP	1.07369	0.921
42DAP/41DAP	1.0866	0.478
43DAP/42DAP	1.10009	0.212
47DAP/43DAP	1.00299	1
52DAP/47DAP	0.97856	0.837
57DAP/52DAP	0.99559	0.869
57DAP/7DAP	0.87803	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98194	0.55
17DAP/reference	0.93842	0.072
27DAP/reference	1.00838	1
39DAP/reference	0.93778	0.049
41DAP/reference	1.01549	0.709
42DAP/reference	0.86093	0.01
43DAP/reference	0.9412	0.23
47DAP/reference	1.81823	0.106
52DAP/reference	0.93482	0.254
57DAP/reference	0.98294	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83014	0.045
17DAP/reference	1.41337	0.025
27DAP/reference	1.71457	0.013
39DAP/reference	1.69129	0.011
41DAP/reference	1.77056	0.005
42DAP/reference	1.67325	0.015
43DAP/reference	1.11567	0.473
47DAP/reference	1.31916	0.051
52DAP/reference	1.47305	0.006
57DAP/reference	1.0052	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0111	1
17DAP/reference	1.0078	0.956
27DAP/reference	0.90191	0.092
39DAP/reference	0.97363	0.464
41DAP/reference	1.00326	0.826
42DAP/reference	1.20943	0.391
43DAP/reference	1.55703	0.219
47DAP/reference	2.50109	0.008
52DAP/reference	1.59517	0.205
57DAP/reference	2.92939	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0258	0.966
26DAP/20DAP	1.48389	0.322
34DAP/26DAP	0.9613	0.92
51DAP/34DAP	1.4117	0.04
52DAP/51DAP	1.00051	1
53DAP/52DAP	0.97927	0.882
55DAP/53DAP	0.96495	0.663
57DAP/55DAP	1.12844	0.898
62DAP/57DAP	0.74734	0.003
68DAP/62DAP	1.06984	0.912
68DAP/14DAP	1.32538	0.091

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84705	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86956	0.356
Mature Green Tomato/Ripe Tomato	1.40697	0.299
Immature Eggplant/Mature Eggplant	0.9245	0.594
Ripe Pepper/Ripe Tomato	0.76012	0.293
Mature Eggplant/Ripe Tomato	0.91649	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.782	0.613
1-1-2/M82	1.01842	1
12-2/M82	1.17064	0.448
12-4/M82	0.95486	1
1-3/M82	1.2391	0.26
2-1-1/M82	1.03514	1
2-1/M82	0.69747	0.322
2-6/M82	1.17554	0.695
3-2/M82	1.13834	0.388
4-1-1/M82	0.95908	1
4-1/M82	0.87026	1
4-3-2/M82	1.2396	0.241
4-3/M82	1.34483	0.268
5-3/M82	0.98748	1
6-2/M82	1.01401	1
6-3/M82	1.06301	1
7-1/M82	0.93766
7-2/M82	0.83169	0.881
9-3-2/M82	1.01002	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02725	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.95774	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.89577
IL1-4/WTpooled	0.98071	1
WT/WTpooled	N/A	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	1.01977	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00792	0.921
DC3000/delta hrp 6h	0.97725	0.95
DC3000/delta hrp 12h	1.10136	1
DC3000/delta hrp 24h	0.52569	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.42741	0.068
DC3000 delta B/DC3000 delta AB	1.27577	0.166

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02168	1
Exp 36h	1.46435	0.489
Exp 60h	1.53018	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.0055	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	0.70879
Var 60h I row2-row1	1.04322
Var 60h NI row2-row1	0.92126	1
Time course 0hI-0hNI	0.84361
Time course 12hI-12hNI	0.98497
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.02646	0.798
transgenic ySAMdc/azygous control (breaker)	0.90703	0.49
transgenic ySAMdc/azygous control (red)	0.90253	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07285	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60624	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87833	0.172
Manapal/WT (break)	1.02842	1
Manapal/WT (red)	0.79407	0.181