Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.4859	0.017
27DAP/17DAP	1.09403	0.88
39DAP/27DAP	1.06002	0.841
41DAP/39DAP	0.93995	0.739
42DAP/41DAP	0.80986	0.774
43DAP/42DAP	0.93226	0.833
47DAP/43DAP	1.00881	0.89
52DAP/47DAP	1.13337	0.699
57DAP/52DAP	0.92024	0.879

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10009	0.685
17DAP/reference	1.08494	0.653
27DAP/reference	0.98434	0.694
39DAP/reference	0.92339	0.391
41DAP/reference	1.15876	0.241
42DAP/reference	1.21008	1
43DAP/reference	1.00007	0.924
47DAP/reference	1.15985	0.167
52DAP/reference	1.05224	0.633
57DAP/reference	0.84135	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70144	0.06
27DAP/17DAP	1.02383	0.98
39DAP/27DAP	1.15707	0.41
41DAP/39DAP	1.07593	0.753
42DAP/41DAP	1.11413	0.354
43DAP/42DAP	1.15852	0.103
47DAP/43DAP	1.01957	0.973
52DAP/47DAP	1.09478	0.718
57DAP/52DAP	1.34034	0.055
57DAP/7DAP	1.60928

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17003	0.263
17DAP/reference	1.1371	0.199
27DAP/reference	1.14738	0.049
39DAP/reference	1.00576	1
41DAP/reference	1.06274	0.524
42DAP/reference	1.06527	0.534
43DAP/reference	1.10381	0.289
47DAP/reference	1.12006	0.395
52DAP/reference	0.97042	0.477
57DAP/reference	1.36659	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23109	0.167
17DAP/reference	1.13298	0.543
27DAP/reference	1.33784	0.022
39DAP/reference	1.13703	0.188
41DAP/reference	1.13796	0.72
42DAP/reference	1.30551	0.034
43DAP/reference	1.14239	0.308
47DAP/reference	1.37238	0.013
52DAP/reference	1.32118	0.053
57DAP/reference	1.44308	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62068	0.015
17DAP/reference	1.18522	0.163
27DAP/reference	1.32788	0.045
39DAP/reference	1.14536	0.163
41DAP/reference	1.1128	0.397
42DAP/reference	1.08977	0.51
43DAP/reference	0.91993	0.365
47DAP/reference	1.08407	0.704
52DAP/reference	0.92576	0.493
57DAP/reference	1.13589	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.301	0.966
26DAP/20DAP	0.92826	1
34DAP/26DAP	1.0354	1
51DAP/34DAP	0.9995	0.957
52DAP/51DAP	1.16888	0.335
53DAP/52DAP	1.13129	0.37
55DAP/53DAP	1.11861	0.737
57DAP/55DAP	1.26306	0.764
62DAP/57DAP	1.04459	1
68DAP/62DAP	0.52916	0.177
68DAP/14DAP	0.59295	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0218	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.30686	0.026
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.09824	0.224
Mature Eggplant/Ripe Tomato	0.57992	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.0048	1
12-2/M82	1.66258
12-4/M82	0.85896	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.07123
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.06097	1
4-3/M82	N/A	N/A
5-3/M82	1.20293	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.41767	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	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.76748	0.418
IL12-4/WTpooled	1.00906	1
IL1-4/WTpooled	0.94083	0.834
WT/WTpooled	1.04237	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	1.06798	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02156	1
DC3000/delta hrp 6h	1.17431	1
DC3000/delta hrp 12h	1.25684	1
DC3000/delta hrp 24h	2.47441	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44112	0.042
DC3000 delta B/DC3000 delta AB	1.20884	0.183

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	1.03863	1
Var 0h	0.62726	0.259
Var 12h I row2-row1	1.43394	0.272
Var 12h NI row2-row1	1.06589	0.649
Var 36h I row2-row1	0.88397	0.438
Var 36h NI row2-row1	1.20595	0.482
Var 60h I row2-row1	0.65075	0.306
Var 60h NI row2-row1	1.26274	0.691
Time course 0hI-0hNI	1.08125	0.799
Time course 12hI-12hNI	1.21524	0.047
Time course 36hI-36hNI	1.20714	0.009
Time course 60hI-60hNI	1.15657	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)	1.70052	0.612
transgenic ySAMdc/azygous control (breaker)	0.46477	0.131
transgenic ySAMdc/azygous control (red)	1.20224	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02739	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08681	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.70007	1
Manapal/WT (break)	0.68191	1
Manapal/WT (red)	0.48605	0.188