Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.10.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80972	0.238
27DAP/17DAP	0.92224	0.833
39DAP/27DAP	1.02278	0.798
41DAP/39DAP	0.7248	0.103
42DAP/41DAP	0.95437	1
43DAP/42DAP	1.14504	0.867
47DAP/43DAP	0.84888	0.522
52DAP/47DAP	1.15284	0.646
57DAP/52DAP	1.13141	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39172	0.023
17DAP/reference	1.01616	0.904
27DAP/reference	0.94541	0.457
39DAP/reference	0.88501	0.194
41DAP/reference	1.07093	0.855
42DAP/reference	2.60208	0.001
43DAP/reference	1.07617	0.73
47DAP/reference	1.40285	0.018
52DAP/reference	1.18869	0.548
57DAP/reference	1.12015	0.18

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17779	0.445
27DAP/17DAP	0.87274	0.259
39DAP/27DAP	0.83852	0.092
41DAP/39DAP	1.07158	0.774
42DAP/41DAP	0.9101	0.322
43DAP/42DAP	0.95182	0.597
47DAP/43DAP	1.08972	0.432
52DAP/47DAP	1.02053	0.945
57DAP/52DAP	1.10073	0.489
57DAP/7DAP	0.90299	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97216	0.55
17DAP/reference	0.9633	0.22
27DAP/reference	0.91484	0.062
39DAP/reference	1.10643	0.05
41DAP/reference	0.98016	0.431
42DAP/reference	0.94927	0.355
43DAP/reference	1.13067	0.344
47DAP/reference	1.07272	0.618
52DAP/reference	1.15109	0.139
57DAP/reference	1.16263	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95787	0.639
17DAP/reference	1.43505	0.037
27DAP/reference	1.49712	0.044
39DAP/reference	1.60114	0.011
41DAP/reference	1.44878	0.008
42DAP/reference	1.63315	0.008
43DAP/reference	1.23151	0.373
47DAP/reference	1.8787	0.01
52DAP/reference	0.88481	0.04
57DAP/reference	1.8583	0.038

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85336	0.077
17DAP/reference	0.87498	0.214
27DAP/reference	1.10501	0.248
39DAP/reference	0.98588	0.544
41DAP/reference	0.91074	0.237
42DAP/reference	0.96632	0.671
43DAP/reference	1.11556	0.499
47DAP/reference	1.21286	0.73
52DAP/reference	0.99128	0.821
57DAP/reference	1.80888	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02908	1
26DAP/20DAP	1.25937	0.415
34DAP/26DAP	0.96043	0.753
51DAP/34DAP	1.01258	0.988
52DAP/51DAP	0.81214	0.07
53DAP/52DAP	0.93318	0.797
55DAP/53DAP	0.78113	0.35
57DAP/55DAP	1.13856	0.492
62DAP/57DAP	1.13575	0.393
68DAP/62DAP	1.09638	0.885
68DAP/14DAP	0.97132	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72754	0.042

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74485	0.29
Mature Green Tomato/Ripe Tomato	1.47684	0.267
Immature Eggplant/Mature Eggplant	0.73429	0.07
Ripe Pepper/Ripe Tomato	0.64647	0.293
Mature Eggplant/Ripe Tomato	1.01957	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.14222	1
12-2/M82	4.07422
12-4/M82	0.71482	0.619
1-3/M82	N/A	N/A
2-1-1/M82	1.13753	0.764
2-1/M82	0.91856
2-6/M82	1.67422	0.695
3-2/M82	0.90196	0.752
4-1-1/M82	1.42827	1
4-1/M82	1.19983
4-3-2/M82	1.03645	1
4-3/M82	1.43587	1
5-3/M82	0.253	0.374
6-2/M82	1.37891
6-3/M82	1.1359	1
7-1/M82	0.54971	0.803
7-2/M82	1.52162	0.385
9-3-2/M82	1.0973	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00968	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02371	1
IL12-4/WTpooled	0.99377	1
IL1-4/WTpooled	0.76154
WT/WTpooled	0.93466	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	0.94981	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.2468	0.894
DC3000/delta hrp 6h	0.68805	0.937
DC3000/delta hrp 12h	1.20622
DC3000/delta hrp 24h	1.11432	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.24204	0.032
DC3000 delta B/DC3000 delta AB	0.34317	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06398	1
Exp 36h	1.04574	1
Exp 60h	1.01491	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01817	1
Var 0h	1.16091	0.782
Var 12h I row2-row1	0.72734	0.357
Var 12h NI row2-row1	0.93675	0.627
Var 36h I row2-row1	0.76034	0.805
Var 36h NI row2-row1	1.07238	1
Var 60h I row2-row1	1.03232	1
Var 60h NI row2-row1	1.01334	1
Time course 0hI-0hNI	1.06288	0.764
Time course 12hI-12hNI	0.99512	1
Time course 36hI-36hNI	0.99532	0.73
Time course 60hI-60hNI	0.26843	0.006

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)	1.15086	0.271
transgenic ySAMdc/azygous control (breaker)	0.62201	0.142
transgenic ySAMdc/azygous control (red)	1.1556	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.49969	0.03

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.39599	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83118	0.172
Manapal/WT (break)	0.59414	0.333
Manapal/WT (red)	0.47495	0.181