Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.8.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86321	0.347
27DAP/17DAP	0.98048	0.996
39DAP/27DAP	1.3027	0.649
41DAP/39DAP	0.96931	0.868
42DAP/41DAP	1.24159	0.685
43DAP/42DAP	0.9303	0.864
47DAP/43DAP	0.49408	0.049
52DAP/47DAP	1.3549	0.821
57DAP/52DAP	1.09156	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91875	0.224
17DAP/reference	1.07795	0.08
27DAP/reference	0.95422	0.471
39DAP/reference	1.01113	1
41DAP/reference	1.13381	0.111
42DAP/reference	0.93072	0.072
43DAP/reference	1.08479	0.089
47DAP/reference	0.8194	0.003
52DAP/reference	0.78143	0.025
57DAP/reference	0.79496	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05147	0.934
27DAP/17DAP	1.05523	0.928
39DAP/27DAP	1.06332	0.698
41DAP/39DAP	0.85256	0.434
42DAP/41DAP	1.01356	0.899
43DAP/42DAP	0.89697	0.269
47DAP/43DAP	0.73239	0.021
52DAP/47DAP	0.89873	0.512
57DAP/52DAP	0.94073	0.603
57DAP/7DAP	0.96042	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82509	0.069
17DAP/reference	0.78665	0.056
27DAP/reference	1.06351	0.804
39DAP/reference	0.99935	0.745
41DAP/reference	0.93889	0.311
42DAP/reference	0.83779	0.117
43DAP/reference	0.85457	0.192
47DAP/reference	0.88558	0.293
52DAP/reference	0.7656	0.035
57DAP/reference	1.02874	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08674	0.597
17DAP/reference	1.08001	0.264
27DAP/reference	0.92899	0.34
39DAP/reference	0.89491	0.235
41DAP/reference	0.9748	0.459
42DAP/reference	0.84952	0.028
43DAP/reference	1.22903	0.202
47DAP/reference	0.93017	0.178
52DAP/reference	0.98545	0.537
57DAP/reference	1.2672	0.119

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89971	0.214
17DAP/reference	0.95682	0.56
27DAP/reference	1.17455	0.171
39DAP/reference	1.0504	0.67
41DAP/reference	0.87781	0.119
42DAP/reference	0.7461	0.059
43DAP/reference	0.73202	0.039
47DAP/reference	1.05827	0.966
52DAP/reference	0.94332	0.518
57DAP/reference	0.65819	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11506	0.966
26DAP/20DAP	1.04854	0.941
34DAP/26DAP	1.09142	1
51DAP/34DAP	1.07239	0.795
52DAP/51DAP	0.8624	1
53DAP/52DAP	0.91277	0.75
55DAP/53DAP	0.49349	0.022
57DAP/55DAP	0.91967	0.658
62DAP/57DAP	0.94254	0.871
68DAP/62DAP	0.81248	0.345
68DAP/14DAP	0.735	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.60224	0.184

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.60408	0.187
Mature Green Tomato/Ripe Tomato	1.96499	0.04
Immature Eggplant/Mature Eggplant	1.472
Ripe Pepper/Ripe Tomato	1.86596	1
Mature Eggplant/Ripe Tomato	2.12207	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97813	0.961
1-1-2/M82	0.85819	1
12-2/M82	1.18668	0.61
12-4/M82	1.30596
1-3/M82	0.90267	0.441
2-1-1/M82	1.00158
2-1/M82	1.60365
2-6/M82	1.07635
3-2/M82	1.13422
4-1-1/M82	N/A	N/A
4-1/M82	1.0942
4-3-2/M82	0.79374	0.487
4-3/M82	0.94718	1
5-3/M82	1.09172	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.17514
7-2/M82	1.04237	1
9-3-2/M82	0.90666

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80487	0.321
IL2-6/WTpooled	1.13031	0.46
IL7-5/WTpooled	1.25001	1
IL7-3/WTpooled	0.96167	1
IL12-4/WTpooled	0.95146	0.71
IL1-4/WTpooled	1.59819	0.426
WT/WTpooled	0.96684	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	1.12805	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03095	0.921
DC3000/delta hrp 6h	0.82037	0.947
DC3000/delta hrp 12h	1.20329	1
DC3000/delta hrp 24h	1.1084	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15672
DC3000 delta B/DC3000 delta AB	1.06413	0.655

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.95746	0.879
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	1.01819	1
Var 0h	0.73688	0.933
Var 12h I row2-row1	1.05216	0.654
Var 12h NI row2-row1	1.21109	0.649
Var 36h I row2-row1	0.92359	1
Var 36h NI row2-row1	1.12364	1
Var 60h I row2-row1	0.80359	0.293
Var 60h NI row2-row1	0.98559	1
Time course 0hI-0hNI	0.97674	0.911
Time course 12hI-12hNI	0.98532	0.931
Time course 36hI-36hNI	1.06956	0.28
Time course 60hI-60hNI	1.1056	0.495

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)	1.06072	0.256
transgenic ySAMdc/azygous control (breaker)	1.09129	1
transgenic ySAMdc/azygous control (red)	0.96916	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01191	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95618	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89299	1
Manapal/WT (break)	0.81882	0.333
Manapal/WT (red)	1.05904	1