Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.9.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19957	0.739
27DAP/17DAP	1.11349	0.849
39DAP/27DAP	1.20606	0.732
41DAP/39DAP	1.15566	0.696
42DAP/41DAP	1.17221	0.931
43DAP/42DAP	0.88693	0.775
47DAP/43DAP	0.8924	0.603
52DAP/47DAP	0.92299	0.721
57DAP/52DAP	1.1101	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00918	0.771
17DAP/reference	1.07558	0.33
27DAP/reference	1.05053	0.405
39DAP/reference	1.10418	0.104
41DAP/reference	1.15855	0.015
42DAP/reference	0.94401	0.163
43DAP/reference	1.03187	0.787
47DAP/reference	0.9808	0.445
52DAP/reference	0.78448	0.03
57DAP/reference	0.67468	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2797	0.048
27DAP/17DAP	0.95951	0.782
39DAP/27DAP	1.56258	0.066
41DAP/39DAP	0.69753	0.137
42DAP/41DAP	1.08857	0.872
43DAP/42DAP	1.05449	0.664
47DAP/43DAP	0.86438	0.156
52DAP/47DAP	1.02166	0.919
57DAP/52DAP	0.78677	0.091
57DAP/7DAP	1.66373	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89739	0.224
17DAP/reference	1.19775	0.059
27DAP/reference	1.15944	0.371
39DAP/reference	1.37423	0.186
41DAP/reference	0.9618	0.412
42DAP/reference	1.4871	0.037
43DAP/reference	1.6492	0.009
47DAP/reference	1.43042	0.169
52DAP/reference	1.30583	0.052
57DAP/reference	1.60284	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11147	0.319
17DAP/reference	0.96978	0.499
27DAP/reference	0.9616	0.452
39DAP/reference	0.99332	0.554
41DAP/reference	0.83457	0.049
42DAP/reference	0.83992	0.073
43DAP/reference	1.10511	0.647
47DAP/reference	0.89279	0.077
52DAP/reference	1.01584	1
57DAP/reference	1.19689	0.214

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19926	0.237
17DAP/reference	0.91591	0.308
27DAP/reference	0.98867	0.657
39DAP/reference	1.16041	0.046
41DAP/reference	0.92585	0.185
42DAP/reference	1.1226	0.863
43DAP/reference	1.12979	0.858
47DAP/reference	0.94343	0.306
52DAP/reference	2.27437	0.237
57DAP/reference	0.65765	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99288	1
26DAP/20DAP	0.81025	1
34DAP/26DAP	1.22519	0.819
51DAP/34DAP	3.34049	0.022
52DAP/51DAP	0.7289	0.079
53DAP/52DAP	1.90503	0.026
55DAP/53DAP	0.91376	0.5
57DAP/55DAP	0.93576	0.688
62DAP/57DAP	0.94593	0.994
68DAP/62DAP	0.72663	0.049
68DAP/14DAP	0.88169	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12359	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.19345	0.059
Mature Green Tomato/Ripe Tomato	1.04665	0.881
Immature Eggplant/Mature Eggplant	2.25768	0.05
Ripe Pepper/Ripe Tomato	7.07542	0.251
Mature Eggplant/Ripe Tomato	0.71301	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9653	0.944
1-1-2/M82	1.05327	1
12-2/M82	1.08144	1
12-4/M82	1.10266
1-3/M82	0.79517	0.441
2-1-1/M82	1.31989	0.689
2-1/M82	1.2276
2-6/M82	1.22456	0.405
3-2/M82	1.29739	0.549
4-1-1/M82	0.96825	1
4-1/M82	N/A	N/A
4-3-2/M82	1.02448
4-3/M82	0.96109	0.551
5-3/M82	0.92545	1
6-2/M82	1.35528	1
6-3/M82	0.80738	0.619
7-1/M82	1.06775	1
7-2/M82	1.06926	1
9-3-2/M82	1.54342

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.58199
IL2-6/WTpooled	0.8245	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.36195	1
IL12-4/WTpooled	1.07472	0.785
IL1-4/WTpooled	1.03574
WT/WTpooled	1.01512	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	1.47646	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93685	1
DC3000/delta hrp 6h	1.25424	1
DC3000/delta hrp 12h	0.99804	1
DC3000/delta hrp 24h	1.12426	0.143

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.89071	0.042
DC3000 delta B/DC3000 delta AB	1.65434	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.31969	1
Exp 36h	2.08956	0.693
Exp 60h	2.37641	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07206	1
Var 0h	1.10788	0.98
Var 12h I row2-row1	1.0778	0.406
Var 12h NI row2-row1	1.77394	0.649
Var 36h I row2-row1	1.62377	0.305
Var 36h NI row2-row1	0.82667	0.743
Var 60h I row2-row1	0.82307	0.285
Var 60h NI row2-row1	0.77596	0.318
Time course 0hI-0hNI	1.12429	0.63
Time course 12hI-12hNI	1.097	0.811
Time course 36hI-36hNI	3.49607	0.004
Time course 60hI-60hNI	12.2223	0.008

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)	0.83285	0.289
transgenic ySAMdc/azygous control (breaker)	1.41782	0.248
transgenic ySAMdc/azygous control (red)	1.15016	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01296	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95021	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9962	1
Manapal/WT (break)	0.867	0.333
Manapal/WT (red)	0.98143	0.863