Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99161	0.64
27DAP/17DAP	1.84632	0.761
39DAP/27DAP	1.51932	0.906
41DAP/39DAP	1.72318	0.929
42DAP/41DAP	1.44634	1
43DAP/42DAP	1.56138	0.937
47DAP/43DAP	2.18394	0.909
52DAP/47DAP	1.65055	0.92
57DAP/52DAP	2.20665	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1345	0.544
17DAP/reference	0.83116	0.008
27DAP/reference	0.82964	0.019
39DAP/reference	1.01038	0.593
41DAP/reference	1.02407	0.714
42DAP/reference	0.95288	0.163
43DAP/reference	0.8542	0.015
47DAP/reference	0.8565	0.03
52DAP/reference	0.94095	0.258
57DAP/reference	0.87521	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88255	0.323
27DAP/17DAP	0.99647	0.943
39DAP/27DAP	1.06163	0.558
41DAP/39DAP	1.09786	0.748
42DAP/41DAP	1.00302	0.869
43DAP/42DAP	1.08002	0.554
47DAP/43DAP	0.91855	0.687
52DAP/47DAP	0.99003	0.93
57DAP/52DAP	1.00223	0.887
57DAP/7DAP	1.36083	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86	0.27
17DAP/reference	1.12718	0.328
27DAP/reference	1.44459	0.012
39DAP/reference	0.89897	0.056
41DAP/reference	1.04186	0.614
42DAP/reference	1.48976	0.006
43DAP/reference	1.06687	0.511
47DAP/reference	0.76584	0.044
52DAP/reference	1.1207	0.081
57DAP/reference	0.89894	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.88442	0.042
17DAP/reference	1.72042	0.009
27DAP/reference	1.44818	0.054
39DAP/reference	1.4409	0.034
41DAP/reference	2.11893	0.009
42DAP/reference	1.2625	0.115
43DAP/reference	1.67238	0.133
47DAP/reference	1.16752	0.069
52DAP/reference	1.57464	0.007
57DAP/reference	1.60778	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96151	0.526
17DAP/reference	1.2394	0.326
27DAP/reference	1.08532	0.51
39DAP/reference	1.14106	0.235
41DAP/reference	1.55979	0.239
42DAP/reference	1.50011	0.007
43DAP/reference	1.30664	0.27
47DAP/reference	1.29426	0.011
52DAP/reference	1.30911	0.121
57DAP/reference	1.29397	0.037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95467	1
26DAP/20DAP	0.86788	0.512
34DAP/26DAP	0.91304	0.627
51DAP/34DAP	1.08202	0.511
52DAP/51DAP	1.08666	0.676
53DAP/52DAP	1.02369	0.91
55DAP/53DAP	1.01094	1
57DAP/55DAP	0.98393	0.911
62DAP/57DAP	1.02369	0.868
68DAP/62DAP	0.88599	0.609
68DAP/14DAP	1.0697	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03309	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.72302	0.119
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.43457	0.224
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.32914	0.503
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	3.11034
1-3/M82	1.44538	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.33384
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.63051
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.58252	1
6-2/M82	0.63587
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.49105	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88682	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95871	0.298
IL12-4/WTpooled	1.05432	0.839
IL1-4/WTpooled	0.91264
WT/WTpooled	1.03783	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	1.43139

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.45203	1
DC3000/delta hrp 6h	1.3505	0.857
DC3000/delta hrp 12h	1.16168	1
DC3000/delta hrp 24h	1.40512	1

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	0.98085	0.916

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96382	1
Exp 36h	1.22627	0.693
Exp 60h	1.65204	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95585	1
Var 0h	0.73419	1
Var 12h I row2-row1	1.07831	0.544
Var 12h NI row2-row1	0.86961	0.713
Var 36h I row2-row1	1.05585	1
Var 36h NI row2-row1	1.15721	1
Var 60h I row2-row1	1.25972	0.543
Var 60h NI row2-row1	1.06357	1
Time course 0hI-0hNI	1.02256	1
Time course 12hI-12hNI	1.0481	0.714
Time course 36hI-36hNI	0.94713	0.373
Time course 60hI-60hNI	1.08261	0.096

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)	1.07895	0.297
transgenic ySAMdc/azygous control (breaker)	0.93155	0.49
transgenic ySAMdc/azygous control (red)	0.90934	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03489	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75276	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78351	0.172
Manapal/WT (break)	0.98672	1
Manapal/WT (red)	1.25192	1