Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05953	1
27DAP/17DAP	1.00045	0.879
39DAP/27DAP	0.72505	0.326
41DAP/39DAP	0.8486	0.457
42DAP/41DAP	0.95471	1
43DAP/42DAP	1.88983	0.248
47DAP/43DAP	1.00019	0.768
52DAP/47DAP	1.61533	0.466
57DAP/52DAP	0.81262	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11275	0.154
17DAP/reference	1.04721	0.21
27DAP/reference	1.04213	0.487
39DAP/reference	0.98849	0.734
41DAP/reference	1.00333	1
42DAP/reference	0.98947	0.469
43DAP/reference	1.02314	0.646
47DAP/reference	0.86471	0.007
52DAP/reference	0.78008	0.05
57DAP/reference	0.79649	0.024

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00571	0.847
27DAP/17DAP	1.131	0.645
39DAP/27DAP	0.88107	0.462
41DAP/39DAP	1.02443	0.875
42DAP/41DAP	1.5153	0.727
43DAP/42DAP	1.03396	0.746
47DAP/43DAP	0.98156	0.911
52DAP/47DAP	0.88176	0.274
57DAP/52DAP	0.96525	0.721
57DAP/7DAP	1.30013	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01121	0.999
17DAP/reference	0.92215	0.064
27DAP/reference	0.74429	0.01
39DAP/reference	0.86869	0.011
41DAP/reference	0.77315	0.011
42DAP/reference	0.73637	0.01
43DAP/reference	0.72619	0.011
47DAP/reference	0.76209	0.066
52DAP/reference	0.70175	0.013
57DAP/reference	0.72996	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23003	0.19
17DAP/reference	1.13015	0.127
27DAP/reference	0.89291	0.188
39DAP/reference	0.88396	0.091
41DAP/reference	0.86684	0.057
42DAP/reference	0.82755	0.013
43DAP/reference	0.85893	0.051
47DAP/reference	0.87749	0.03
52DAP/reference	0.89374	0.005
57DAP/reference	0.93678	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11188	0.153
17DAP/reference	1.11213	0.182
27DAP/reference	0.94917	0.14
39DAP/reference	0.87558	0.021
41DAP/reference	0.85177	0.037
42DAP/reference	0.85657	0.172
43DAP/reference	0.88768	0.098
47DAP/reference	1.17651	0.008
52DAP/reference	0.78651	0.158
57DAP/reference	0.82244	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9709	1
26DAP/20DAP	1.24754	0.453
34DAP/26DAP	0.75982	0.448
51DAP/34DAP	1.83573	0.032
52DAP/51DAP	0.94298	1
53DAP/52DAP	1.53306	0.027
55DAP/53DAP	0.77406	0.188
57DAP/55DAP	0.8993	0.575
62DAP/57DAP	1.05974	0.833
68DAP/62DAP	0.93491	0.7
68DAP/14DAP	1.03902	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.40612	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89787	0.447
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.48794	0.063
Ripe Pepper/Ripe Tomato	1.56796	1
Mature Eggplant/Ripe Tomato	2.37846	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89177	0.638
1-1-2/M82	0.87696	1
12-2/M82	0.83952	0.692
12-4/M82	1.01632	1
1-3/M82	1.0215
2-1-1/M82	0.80982	0.465
2-1/M82	0.62306	0.345
2-6/M82	1.11581	0.695
3-2/M82	1.25603
4-1-1/M82	1.04827	1
4-1/M82	0.6067
4-3-2/M82	N/A	N/A
4-3/M82	1.30834	1
5-3/M82	1.08629	1
6-2/M82	1.34745
6-3/M82	0.88818
7-1/M82	1.03107
7-2/M82	1.22612	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16545	0.277
IL2-6/WTpooled	0.95146	0.473
IL7-5/WTpooled	0.93189	1
IL7-3/WTpooled	1.08613	0.362
IL12-4/WTpooled	1.10656	0.538
IL1-4/WTpooled	1.03375	1
WT/WTpooled	0.95818	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	1.06262	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93886	1
DC3000/delta hrp 6h	1.15394	1
DC3000/delta hrp 12h	0.94092	1
DC3000/delta hrp 24h	0.65499	0.05

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7986	0.027
DC3000 delta B/DC3000 delta AB	0.90152	0.157

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9925	1
Var 0h	0.52168	1
Var 12h I row2-row1	1.03017	0.795
Var 12h NI row2-row1	0.95043	0.488
Var 36h I row2-row1	1.19546	0.742
Var 36h NI row2-row1	1.00763	1
Var 60h I row2-row1	0.75883	0.285
Var 60h NI row2-row1	1.04577	1
Time course 0hI-0hNI	0.97172	0.808
Time course 12hI-12hNI	1.04158	0.779
Time course 36hI-36hNI	1.11666	0.028
Time course 60hI-60hNI	2.00758	0.013

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)	1.07493	0.286
transgenic ySAMdc/azygous control (breaker)	1.54035	0.248
transgenic ySAMdc/azygous control (red)	2.03993	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93649	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.59978	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.88828	0.083
Manapal/WT (break)	3.90587	0.13
Manapal/WT (red)	4.13275	0.137