Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.12.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29194	0.523
27DAP/17DAP	0.96481	0.934
39DAP/27DAP	1.28517	0.489
41DAP/39DAP	0.77083	0.184
42DAP/41DAP	0.92225	1
43DAP/42DAP	0.98036	0.925
47DAP/43DAP	0.85409	0.522
52DAP/47DAP	0.86706	0.618
57DAP/52DAP	0.85322	0.67

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.2303	0.006
17DAP/reference	1.31617	0.282
27DAP/reference	0.89954	0.215
39DAP/reference	1.23591	0.27
41DAP/reference	1.25481	0.079
42DAP/reference	1.69399	0.001
43DAP/reference	1.2294	0.035
47DAP/reference	1.17507	0.318
52DAP/reference	0.95987	0.449
57DAP/reference	1.05349	0.478

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07218	0.5
27DAP/17DAP	0.82736	0.508
39DAP/27DAP	0.8964	0.106
41DAP/39DAP	1.17997	0.65
42DAP/41DAP	0.94047	0.469
43DAP/42DAP	1.02787	0.699
47DAP/43DAP	0.97012	0.712
52DAP/47DAP	1.06	0.816
57DAP/52DAP	1.10773	0.611
57DAP/7DAP	0.76201	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42341	0.063
17DAP/reference	1.22847	0.013
27DAP/reference	1.18712	0.088
39DAP/reference	1.32537	0.141
41DAP/reference	1.14955	0.723
42DAP/reference	1.21338	0.405
43DAP/reference	1.09588	0.746
47DAP/reference	1.41732	0.093
52DAP/reference	1.15268	0.183
57DAP/reference	1.08154	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57803	0.065
17DAP/reference	2.07486	0.01
27DAP/reference	1.6518	0.022
39DAP/reference	1.38012	0.059
41DAP/reference	1.34723	0.215
42DAP/reference	1.51862	0.039
43DAP/reference	1.3061	0.453
47DAP/reference	1.55237	0.012
52DAP/reference	1.18753	0.03
57DAP/reference	1.30342	0.091

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37429	0.025
17DAP/reference	1.4412	0.093
27DAP/reference	1.1721	0.149
39DAP/reference	1.20677	0.031
41DAP/reference	1.25241	0.029
42DAP/reference	1.41688	0.028
43DAP/reference	1.52515	0.121
47DAP/reference	1.37471	0.053
52DAP/reference	1.43035	0.167
57DAP/reference	1.29247	0.255

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.51641
26DAP/20DAP	0.96252	1
34DAP/26DAP	1.31502	1
51DAP/34DAP	0.93728	0.587
52DAP/51DAP	1.27014	0.335
53DAP/52DAP	0.77248	0.202
55DAP/53DAP	1.63672	0.039
57DAP/55DAP	0.93201	0.765
62DAP/57DAP	1.12727	1
68DAP/62DAP	1.40374	1
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18347	0.415

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18731	0.176
Mature Green Tomato/Ripe Tomato	1.86822	0.026
Immature Eggplant/Mature Eggplant	1.09329	0.165
Ripe Pepper/Ripe Tomato	1.52493	1
Mature Eggplant/Ripe Tomato	1.54561

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	2.44145
4-3-2/M82	1.6055	0.241
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.47892	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96102	1
IL12-4/WTpooled	1.63022
IL1-4/WTpooled	1.33913
WT/WTpooled	0.89917

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	0.89638	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.06966	1
DC3000/delta hrp 12h	1.09859	1
DC3000/delta hrp 24h	0.39248

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02631	0.648
DC3000 delta B/DC3000 delta AB	1.03877	0.571

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98351	1
Exp 36h	0.8473	0.749
Exp 60h	0.78798	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00166	1
Var 0h	1.0113	1
Var 12h I row2-row1	0.95407	0.856
Var 12h NI row2-row1	0.91583	0.82
Var 36h I row2-row1	1.06111	0.601
Var 36h NI row2-row1	1.09362	1
Var 60h I row2-row1	0.986	1
Var 60h NI row2-row1	0.88691	0.818
Time course 0hI-0hNI	0.96989	0.801
Time course 12hI-12hNI	0.96727	0.618
Time course 36hI-36hNI	0.91546	0.041
Time course 60hI-60hNI	0.52965	0.006

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)	0.92982	0.324
transgenic ySAMdc/azygous control (breaker)	0.88345	0.49
transgenic ySAMdc/azygous control (red)	1.11708	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97685	0.107

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76446	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23651	0.105
Manapal/WT (break)	1.08034	1
Manapal/WT (red)	1.11664	1