Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.10.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9387	0.664
27DAP/17DAP	0.96289	0.863
39DAP/27DAP	1.22348	0.539
41DAP/39DAP	0.9634	0.815
42DAP/41DAP	0.99914	1
43DAP/42DAP	1.06136	1
47DAP/43DAP	0.70597	0.122
52DAP/47DAP	1.03783	0.96
57DAP/52DAP	1.14467	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32932	0.018
17DAP/reference	0.91041	0.224
27DAP/reference	0.84053	0.134
39DAP/reference	0.98	0.762
41DAP/reference	0.92343	0.267
42DAP/reference	1.14404	1
43DAP/reference	1.03742	0.899
47DAP/reference	1.14273	0.035
52DAP/reference	1.02676	0.709
57DAP/reference	1.23379	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17022	0.044
27DAP/17DAP	0.70765	0.259
39DAP/27DAP	0.92212	0.607
41DAP/39DAP	1.41846	0.484
42DAP/41DAP	1.08127	1
43DAP/42DAP	1.0109	1
47DAP/43DAP	1.10501	0.52
52DAP/47DAP	0.89061	0.528
57DAP/52DAP	0.76627	0.283
57DAP/7DAP	0.77525	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.10532	0.024
17DAP/reference	1.49329	0.012
27DAP/reference	1.14407	0.246
39DAP/reference	1.26869	0.014
41DAP/reference	1.35168	0.034
42DAP/reference	1.42229	0.024
43DAP/reference	1.34007	0.01
47DAP/reference	1.36956	0.027
52DAP/reference	1.32388	0.017
57DAP/reference	1.31392	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13237	0.355
17DAP/reference	1.15697	0.216
27DAP/reference	1.21181	0.073
39DAP/reference	1.29328	0.073
41DAP/reference	1.15014	0.344
42DAP/reference	1.16019	0.162
43DAP/reference	0.95823	0.468
47DAP/reference	0.9581	0.423
52DAP/reference	1.03598	0.789
57DAP/reference	0.86803	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.9824	0.015
17DAP/reference	1.36318	0.283
27DAP/reference	1.07499	0.237
39DAP/reference	1.22468	0.008
41DAP/reference	1.13854	0.112
42DAP/reference	1.13179	0.307
43DAP/reference	1.62182	0.019
47DAP/reference	0.94839	0.371
52DAP/reference	1.23308	0.182
57DAP/reference	1.24831	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.59847	0.033
26DAP/20DAP	0.95139	1
34DAP/26DAP	0.97927	0.998
51DAP/34DAP	0.9483	0.758
52DAP/51DAP	0.76834	1
53DAP/52DAP	0.95082	0.824
55DAP/53DAP	0.85916	0.648
57DAP/55DAP	0.63911	0.059
62DAP/57DAP	0.9369	0.871
68DAP/62DAP	1.56935	0.04
68DAP/14DAP	1.47727	0.139

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.88631	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.10049	0.075
Mature Green Tomato/Ripe Tomato	1.88827	0.026
Immature Eggplant/Mature Eggplant	1.04514	0.462
Ripe Pepper/Ripe Tomato	1.69944	0.256
Mature Eggplant/Ripe Tomato	1.64295	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06903	0.877
1-1-2/M82	1.13024	1
12-2/M82	0.87522	0.721
12-4/M82	0.90395	1
1-3/M82	1.47693	0.479
2-1-1/M82	1.05999	1
2-1/M82	N/A	N/A
2-6/M82	1.40869	0.364
3-2/M82	1.20329
4-1-1/M82	0.96241	1
4-1/M82	0.96419
4-3-2/M82	1.3818	0.508
4-3/M82	1.28739	1
5-3/M82	1.17725	1
6-2/M82	1.35787
6-3/M82	N/A	N/A
7-1/M82	0.88979
7-2/M82	1.54515	0.282
9-3-2/M82	1.33673	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.5683
IL2-6/WTpooled	0.97514	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0384	1
IL12-4/WTpooled	0.79534	0.71
IL1-4/WTpooled	0.9401	0.415
WT/WTpooled	1.05477	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	1.01685	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01298	1
DC3000/delta hrp 6h	1.06974	1
DC3000/delta hrp 12h	1.0311	1
DC3000/delta hrp 24h	0.85717	0.148

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80073
DC3000 delta B/DC3000 delta AB	0.86725	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05727	1
Exp 36h	0.88935	0.82
Exp 60h	0.89156	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9857	1
Var 0h	0.5937	0.457
Var 12h I row2-row1	0.88917	0.467
Var 12h NI row2-row1	1.02539	1
Var 36h I row2-row1	0.97768	1
Var 36h NI row2-row1	1.02488	1
Var 60h I row2-row1	0.89715	0.582
Var 60h NI row2-row1	0.81086	0.756
Time course 0hI-0hNI	0.98834	0.991
Time course 12hI-12hNI	0.91914	0.201
Time course 36hI-36hNI	0.8778	0.056
Time course 60hI-60hNI	0.4803	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)	0.91542	0.362
transgenic ySAMdc/azygous control (breaker)	0.94643	0.49
transgenic ySAMdc/azygous control (red)	1.09318	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95642	0.101

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71512	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20971	0.105
Manapal/WT (break)	1.0381	1
Manapal/WT (red)	0.88442	0.216