Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.1.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.83324	0.041
27DAP/17DAP	1.07577	0.88
39DAP/27DAP	1.56868	0.141
41DAP/39DAP	0.80747	0.303
42DAP/41DAP	1.57081	0.051
43DAP/42DAP	0.93896	0.877
47DAP/43DAP	1.63269	0.215
52DAP/47DAP	1.0608	0.924
57DAP/52DAP	1.11082	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82537	0.145
17DAP/reference	1.18541	0.178
27DAP/reference	1.49541	0.01
39DAP/reference	1.32989	0.033
41DAP/reference	1.17998	0.133
42DAP/reference	1.75509	0.001
43DAP/reference	1.66963	0.01
47DAP/reference	2.80577	0.001
52DAP/reference	3.43475	0.007
57DAP/reference	2.29594	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.75877	0.036
27DAP/17DAP	0.80135	0.121
39DAP/27DAP	1.00848	0.832
41DAP/39DAP	0.81016	0.246
42DAP/41DAP	1.07345	0.886
43DAP/42DAP	1.16923	0.03
47DAP/43DAP	0.96587	0.833
52DAP/47DAP	1.64264	0.063
57DAP/52DAP	1.39227	0.222
57DAP/7DAP	2.14884	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99681	0.758
17DAP/reference	1.33905	0.012
27DAP/reference	1.14787	0.03
39DAP/reference	1.83077	0.005
41DAP/reference	1.49885	0.02
42DAP/reference	1.61932	0.011
43DAP/reference	2.15505	0.007
47DAP/reference	1.52722	0.055
52DAP/reference	1.74191	0.009
57DAP/reference	2.11949	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70866	0.048
17DAP/reference	1.35772	0.048
27DAP/reference	1.11437	0.288
39DAP/reference	1.60341	0.015
41DAP/reference	1.30127	0.074
42DAP/reference	1.58296	0.015
43DAP/reference	1.12115	0.641
47DAP/reference	1.67761	0.009
52DAP/reference	1.21397	0.079
57DAP/reference	1.32038	0.229

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84559	0.158
17DAP/reference	0.86623	0.144
27DAP/reference	1.09204	0.237
39DAP/reference	1.02665	0.773
41DAP/reference	1.14108	0.115
42DAP/reference	1.58958	0.007
43DAP/reference	1.89812	0.008
47DAP/reference	2.27778	0.007
52DAP/reference	2.4419	0.027
57DAP/reference	5.89058	0.005

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05945	1
26DAP/20DAP	1.40285
34DAP/26DAP	1.54838	0.154
51DAP/34DAP	1.69018	0.637
52DAP/51DAP	0.95731	1
53DAP/52DAP	1.27202	0.58
55DAP/53DAP	0.9832	0.852
57DAP/55DAP	0.73955	0.118
62DAP/57DAP	0.89513	0.466
68DAP/62DAP	0.9119	0.135
68DAP/14DAP	0.82824	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.29553	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11296	0.287
Mature Green Tomato/Ripe Tomato	0.51274	0.2
Immature Eggplant/Mature Eggplant	0.90421	0.448
Ripe Pepper/Ripe Tomato	0.1202	0.224
Mature Eggplant/Ripe Tomato	0.16957	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.42228	0.742
1-1-2/M82	1.26536	1
12-2/M82	1.06956	1
12-4/M82	1.20618	1
1-3/M82	1.77177	0.26
2-1-1/M82	1.01666	1
2-1/M82	0.84135	0.322
2-6/M82	1.16983	0.594
3-2/M82	0.8408	0.752
4-1-1/M82	1.01473	1
4-1/M82	0.87864
4-3-2/M82	1.28015	1
4-3/M82	1.00129	1
5-3/M82	0.94395	1
6-2/M82	0.84115	0.481
6-3/M82	0.93664	1
7-1/M82	0.94551	0.803
7-2/M82	0.92648	0.881
9-3-2/M82	1.3794	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82667
IL2-6/WTpooled	1.00194	1
IL7-5/WTpooled	0.86988	0.483
IL7-3/WTpooled	0.83217	0.418
IL12-4/WTpooled	0.97512	1
IL1-4/WTpooled	0.98138	1
WT/WTpooled	1.11218	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	1.07473	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12606	0.823
DC3000/delta hrp 6h	0.87609	0.95
DC3000/delta hrp 12h	1.98481	1
DC3000/delta hrp 24h	0.90665	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.027
DC3000 delta B/DC3000 delta AB	1.1292	0.429

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02348	1
Exp 36h	0.76647	0.504
Exp 60h	0.837	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02395	1
Var 0h	1.15203	1
Var 12h I row2-row1	0.85086	0.338
Var 12h NI row2-row1	1.16367	0.649
Var 36h I row2-row1	1.21816	1
Var 36h NI row2-row1	1.54418	1
Var 60h I row2-row1	0.9266
Var 60h NI row2-row1	1.05984	0.904
Time course 0hI-0hNI	1.07422	0.486
Time course 12hI-12hNI	0.81744	0.056
Time course 36hI-36hNI	0.577	0.023
Time course 60hI-60hNI	0.91056	0.047

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)	1.13178	0.397
transgenic ySAMdc/azygous control (breaker)	0.60847	0.131
transgenic ySAMdc/azygous control (red)	1.01746	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.24676	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64232	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.5917	0.172
Manapal/WT (break)	1.30477	0.14
Manapal/WT (red)	0.92679	0.229