Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.20.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63964	0.103
27DAP/17DAP	1.054	0.93
39DAP/27DAP	0.93243	0.652
41DAP/39DAP	1.01597	0.841
42DAP/41DAP	0.95414	1
43DAP/42DAP	0.82101	0.759
47DAP/43DAP	1.22765	0.4
52DAP/47DAP	0.96906	0.742
57DAP/52DAP	1.15742	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87673	0.167
17DAP/reference	1.03659	0.546
27DAP/reference	1.08271	0.684
39DAP/reference	1.01602	0.786
41DAP/reference	1.03849	0.714
42DAP/reference	0.8993	0.034
43DAP/reference	0.97168	0.653
47DAP/reference	0.98065	0.445
52DAP/reference	0.9521	0.393
57DAP/reference	0.95859	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80656	0.037
27DAP/17DAP	0.74988	0.537
39DAP/27DAP	1.00605	1
41DAP/39DAP	1.00566	0.921
42DAP/41DAP	0.85346	0.407
43DAP/42DAP	1.1153	0.554
47DAP/43DAP	0.95681	0.902
52DAP/47DAP	1.28352	0.73
57DAP/52DAP	0.97745	0.789
57DAP/7DAP	0.3868

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99916	0.758
17DAP/reference	1.21017	0.084
27DAP/reference	0.99324	0.656
39DAP/reference	0.94904	0.095
41DAP/reference	1.08606	0.701
42DAP/reference	0.97982	0.531
43DAP/reference	0.9464	0.056
47DAP/reference	1.01273	1
52DAP/reference	0.9081	0.213
57DAP/reference	1.05371	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97433	0.706
17DAP/reference	0.95887	0.434
27DAP/reference	0.87992	0.167
39DAP/reference	0.84522	0.129
41DAP/reference	0.89128	0.091
42DAP/reference	1.04482	1
43DAP/reference	1.04292	0.885
47DAP/reference	0.9525	0.319
52DAP/reference	0.80437	0.012
57DAP/reference	0.88134	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96686	0.489
17DAP/reference	0.90245	0.305
27DAP/reference	0.88297	0.102
39DAP/reference	0.79982	0.011
41DAP/reference	0.88676	0.077
42DAP/reference	0.84955	0.049
43DAP/reference	0.81247	0.066
47DAP/reference	0.99855	0.731
52DAP/reference	0.94368	0.573
57DAP/reference	0.84554	0.111

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01747	1
26DAP/20DAP	0.87377	1
34DAP/26DAP	1.49062	0.304
51DAP/34DAP	0.72108	0.24
52DAP/51DAP	1.32246	0.163
53DAP/52DAP	0.83368	0.684
55DAP/53DAP	1.07012	0.989
57DAP/55DAP	1.29042	0.854
62DAP/57DAP	0.94922	0.994
68DAP/62DAP	1.38298	0.185
68DAP/14DAP	1.938	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32842	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.57113
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.90608
Mature Eggplant/Ripe Tomato	1.05804

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97776
1-1-2/M82	1.10259
12-2/M82	N/A	N/A
12-4/M82	1.22586
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	0.96933	1
6-2/M82	N/A	N/A
6-3/M82	0.98833	1
7-1/M82	N/A	N/A
7-2/M82	1.20155
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00581
IL2-6/WTpooled	0.9219	1
IL7-5/WTpooled	1.04451	1
IL7-3/WTpooled	0.9908	1
IL12-4/WTpooled	0.91599	0.581
IL1-4/WTpooled	0.98809	1
WT/WTpooled	0.99753	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	1.02471	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.2265	0.875
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.97355	0.851

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11179	1
DC3000 delta B/DC3000 delta AB	1.31372

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.06216	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.1101
Var 0h	N/A	N/A
Var 12h I row2-row1	0.81866	0.705
Var 12h NI row2-row1	0.98499	1
Var 36h I row2-row1	1.38197	0.309
Var 36h NI row2-row1	1.22993	1
Var 60h I row2-row1	1.04783	1
Var 60h NI row2-row1	0.66661	0.932
Time course 0hI-0hNI	0.88863	0.386
Time course 12hI-12hNI	1.09204	0.567
Time course 36hI-36hNI	1.14996	0.453
Time course 60hI-60hNI	2.69122	0.019

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)	0.91264	0.567
transgenic ySAMdc/azygous control (breaker)	1.35699	0.162
transgenic ySAMdc/azygous control (red)	1.12245	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02144	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0627	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08288	0.09
Manapal/WT (break)	0.67872	0.299
Manapal/WT (red)	1.28272	0.413