Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.7.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7498	0.04
27DAP/17DAP	1.08184	0.91
39DAP/27DAP	2.43758	0.134
41DAP/39DAP	0.66195	0.097
42DAP/41DAP	1.62622	0.595
43DAP/42DAP	0.84169	0.639
47DAP/43DAP	0.73682	0.266
52DAP/47DAP	1.53833	0.913
57DAP/52DAP	2.31324	0.764

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12709	0.735
17DAP/reference	0.71042	0.057
27DAP/reference	0.80459	0.249
39DAP/reference	0.69214	0.081
41DAP/reference	0.47073	0.01
42DAP/reference	0.86189	0.052
43DAP/reference	0.72164	0.013
47DAP/reference	0.6687	0.002
52DAP/reference	0.63365	0.036
57DAP/reference	0.82139	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87147	0.17
27DAP/17DAP	1.08258	0.9
39DAP/27DAP	1.01417	1
41DAP/39DAP	1.07833	1
42DAP/41DAP	1.15311	0.425
43DAP/42DAP	0.93287	0.431
47DAP/43DAP	1.26703	0.713
52DAP/47DAP	0.80424	0.255
57DAP/52DAP	1.06121	0.992
57DAP/7DAP	0.87032	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27513	0.173
17DAP/reference	1.11636	0.269
27DAP/reference	1.2281	0.16
39DAP/reference	1.09607	0.333
41DAP/reference	1.09342	0.977
42DAP/reference	1.14616	0.1
43DAP/reference	1.00681	0.764
47DAP/reference	0.823	0.293
52DAP/reference	1.17879	0.007
57DAP/reference	1.06732	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87393	0.182
17DAP/reference	0.82605	0.077
27DAP/reference	0.90122	0.304
39DAP/reference	0.72431	0.083
41DAP/reference	0.80316	0.108
42DAP/reference	0.77124	0.061
43DAP/reference	0.77864	0.224
47DAP/reference	0.50438	0.01
52DAP/reference	0.39512	0.003
57DAP/reference	0.38103	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44047	0.126
17DAP/reference	1.1582	0.685
27DAP/reference	1.09121	0.487
39DAP/reference	1.17001	0.052
41DAP/reference	0.97133	0.56
42DAP/reference	1.25706	0.424
43DAP/reference	1.19043	0.524
47DAP/reference	0.41646	0.004
52DAP/reference	1.15989	0.862
57DAP/reference	1.53543	0.126

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21231	0.916
26DAP/20DAP	1.14648	0.62
34DAP/26DAP	1.01819	1
51DAP/34DAP	0.70926	0.061
52DAP/51DAP	0.80777	1
53DAP/52DAP	0.98821	0.902
55DAP/53DAP	0.72207	0.021
57DAP/55DAP	1.32383	0.841
62DAP/57DAP	1.27887	0.185
68DAP/62DAP	0.9785	0.885
68DAP/14DAP	1.24013	0.189

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.46224	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.73124	0.203
Mature Green Tomato/Ripe Tomato	1.25748	0.478
Immature Eggplant/Mature Eggplant	1.37165	0.248
Ripe Pepper/Ripe Tomato	1.38426	1
Mature Eggplant/Ripe Tomato	1.46116	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.28398
1-1-2/M82	N/A	N/A
12-2/M82	1.05017
12-4/M82	N/A	N/A
1-3/M82	2.19398
2-1-1/M82	0.86167	0.565
2-1/M82	0.94788
2-6/M82	0.78496	1
3-2/M82	N/A	N/A
4-1-1/M82	1.26715
4-1/M82	N/A	N/A
4-3-2/M82	1.5698	0.241
4-3/M82	1.17057	1
5-3/M82	1.14198	0.572
6-2/M82	0.74978
6-3/M82	0.95642	1
7-1/M82	0.94506
7-2/M82	0.9736
9-3-2/M82	0.97332

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.09552	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18138	0.921
DC3000/delta hrp 6h	0.78054	0.82
DC3000/delta hrp 12h	0.983	1
DC3000/delta hrp 24h	1.12668	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07885	0.408
DC3000 delta B/DC3000 delta AB	1.01709	0.687

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	1.01393	1
Var 0h	0.44196	0.261
Var 12h I row2-row1	0.96168	0.948
Var 12h NI row2-row1	1.02741	1
Var 36h I row2-row1	1.36537	0.339
Var 36h NI row2-row1	0.92789	0.743
Var 60h I row2-row1	1.00612	1
Var 60h NI row2-row1	0.93413	0.977
Time course 0hI-0hNI	0.88281	0.136
Time course 12hI-12hNI	1.00504	0.892
Time course 36hI-36hNI	1.32429	0.025
Time course 60hI-60hNI	1.03332	1

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)	1.01298	0.699
transgenic ySAMdc/azygous control (breaker)	1.24382	1
transgenic ySAMdc/azygous control (red)	1.15894	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.38386	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88609	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.55704	0.307
Manapal/WT (break)	1.48921	0.14
Manapal/WT (red)	1.75165	0.142