Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93545	0.627
27DAP/17DAP	1.15645	0.849
39DAP/27DAP	1.02062	0.857
41DAP/39DAP	1.00699	0.978
42DAP/41DAP	0.95444	1
43DAP/42DAP	1.01259	1
47DAP/43DAP	1.52291	0.584
52DAP/47DAP	1.31612	0.633
57DAP/52DAP	0.86902	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90376	0.125
17DAP/reference	1.01707	0.546
27DAP/reference	1.12363	0.046
39DAP/reference	1.04842	0.368
41DAP/reference	0.95478	0.267
42DAP/reference	0.9027	0.018
43DAP/reference	0.93156	0.135
47DAP/reference	0.97186	0.322
52DAP/reference	0.99788	0.73
57DAP/reference	1.0986	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.58342	0.053
27DAP/17DAP	0.67515	0.1
39DAP/27DAP	1.1985	0.514
41DAP/39DAP	0.90607	0.512
42DAP/41DAP	1.06567	0.935
43DAP/42DAP	0.79029	0.079
47DAP/43DAP	0.87819	0.569
52DAP/47DAP	1.96126	0.048
57DAP/52DAP	2.94135	0.044
57DAP/7DAP	4.6782	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98215	0.613
17DAP/reference	1.08924	0.627
27DAP/reference	1.0186	1
39DAP/reference	1.05297	0.669
41DAP/reference	1.0602	0.593
42DAP/reference	1.03369	1
43DAP/reference	1.01587	0.802
47DAP/reference	1.04476	0.915
52DAP/reference	0.99797	0.74
57DAP/reference	1.10454	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01348	0.93
17DAP/reference	0.85464	0.027
27DAP/reference	0.98414	0.554
39DAP/reference	0.81477	0.019
41DAP/reference	0.99792	0.666
42DAP/reference	0.88291	0.169
43DAP/reference	0.94341	0.37
47DAP/reference	0.98267	0.423
52DAP/reference	0.9325	0.111
57DAP/reference	0.95092	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94523	0.29
17DAP/reference	1.19461	0.279
27DAP/reference	1.10918	0.373
39DAP/reference	1.31467	0.017
41DAP/reference	1.31374	0.086
42DAP/reference	1.06086	0.848
43DAP/reference	0.99893	0.712
47DAP/reference	0.92439	0.183
52DAP/reference	0.69789	0.059
57DAP/reference	0.71341	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9493	0.89
26DAP/20DAP	0.69508	0.512
34DAP/26DAP	N/A	N/A
51DAP/34DAP	1.26629	0.893
52DAP/51DAP	1.51165	0.08
53DAP/52DAP	0.90949	0.712
55DAP/53DAP	1.24456	0.487
57DAP/55DAP	1.06587	0.947
62DAP/57DAP	1.94979	0.833
68DAP/62DAP	0.98067	0.863
68DAP/14DAP	0.86584	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90171	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.13453	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.94535

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15973
1-1-2/M82	0.88834
12-2/M82	0.75578
12-4/M82	0.73824
1-3/M82	1.25308
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	1.15353
5-3/M82	1.32559
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.50606
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91386	0.243
IL2-6/WTpooled	0.84237	1
IL7-5/WTpooled	1.08848	0.67
IL7-3/WTpooled	1.21445	1
IL12-4/WTpooled	1.02063	1
IL1-4/WTpooled	1.03787	1
WT/WTpooled	0.9773	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	1.12023

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10166	0.774
DC3000/delta hrp 6h	1.10944	1
DC3000/delta hrp 12h	1.09785	1
DC3000/delta hrp 24h	1.2016	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.8315	0.589
Exp 60h	1.12286	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00481	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.9328	0.705
Var 12h NI row2-row1	1.04326	1
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	4.61348	1
Var 60h I row2-row1	0.73883	0.832
Var 60h NI row2-row1	1.04043
Time course 0hI-0hNI	1.06494	0.852
Time course 12hI-12hNI	1.31161	0.603
Time course 36hI-36hNI	1.90271	0.147
Time course 60hI-60hNI	0.89636	0.319

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)	1.11041	0.331
transgenic ySAMdc/azygous control (breaker)	2.51738	0.178
transgenic ySAMdc/azygous control (red)	1.52538	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98525	0.534

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84642	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.60689	0.172
Manapal/WT (break)	0.78331	1
Manapal/WT (red)	0.56581	0.181