Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.16.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88382	0.436
27DAP/17DAP	1.08381	0.902
39DAP/27DAP	1.30958	0.53
41DAP/39DAP	0.94208	0.739
42DAP/41DAP	1.00157	1
43DAP/42DAP	0.94132	0.705
47DAP/43DAP	1.31341	0.542
52DAP/47DAP	0.94908	0.793
57DAP/52DAP	0.98062	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91435	0.162
17DAP/reference	1.03851	0.675
27DAP/reference	1.03569	0.487
39DAP/reference	0.97786	0.691
41DAP/reference	1.0492	0.714
42DAP/reference	0.82486	0.002
43DAP/reference	0.92791	0.346
47DAP/reference	0.84982	0.013
52DAP/reference	0.82039	0.036
57DAP/reference	0.87141	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99258	0.763
27DAP/17DAP	0.92392	0.854
39DAP/27DAP	1.01885	1
41DAP/39DAP	0.97729	0.959
42DAP/41DAP	1.11452	0.8
43DAP/42DAP	1.28484	0.034
47DAP/43DAP	0.94603	0.534
52DAP/47DAP	0.84331	0.334
57DAP/52DAP	1.13365	0.813
57DAP/7DAP	1.05856	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95245	0.326
17DAP/reference	0.8912	0.108
27DAP/reference	0.74144	0.012
39DAP/reference	0.72144	0.017
41DAP/reference	0.74969	0.017
42DAP/reference	0.71762	0.011
43DAP/reference	0.74113	0.016
47DAP/reference	0.96258	0.504
52DAP/reference	0.90036	0.15
57DAP/reference	0.86019	0.025

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8479	0.034
17DAP/reference	0.86392	0.109
27DAP/reference	0.89112	0.212
39DAP/reference	0.78814	0.038
41DAP/reference	0.82358	0.064
42DAP/reference	0.8409	0.055
43DAP/reference	0.95626	0.468
47DAP/reference	0.92321	0.173
52DAP/reference	0.93089	0.259
57DAP/reference	0.98886	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93803	0.29
17DAP/reference	0.98437	0.709
27DAP/reference	0.79128	0.046
39DAP/reference	0.82851	0.054
41DAP/reference	0.85079	0.064
42DAP/reference	0.80002	0.016
43DAP/reference	0.86405	0.116
47DAP/reference	1.05761	0.519
52DAP/reference	0.7722	0.144
57DAP/reference	0.8135	0.06

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01959	1
26DAP/20DAP	0.96763	1
34DAP/26DAP	1.3352	0.819
51DAP/34DAP	1.11404	0.654
52DAP/51DAP	1.0464	0.904
53DAP/52DAP	1.19017	0.356
55DAP/53DAP	0.81907	0.293
57DAP/55DAP	1.00215	0.855
62DAP/57DAP	0.99236	0.994
68DAP/62DAP	0.90739	0.769
68DAP/14DAP	1.0531	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89914	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.3562	0.124
Mature Green Tomato/Ripe Tomato	1.14221	1
Immature Eggplant/Mature Eggplant	1.27721
Ripe Pepper/Ripe Tomato	1.07437	1
Mature Eggplant/Ripe Tomato	0.87415	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.36607	0.304
1-1-2/M82	0.97574	1
12-2/M82	0.79711
12-4/M82	0.93905	1
1-3/M82	N/A	N/A
2-1-1/M82	1.08256
2-1/M82	1.54828	0.345
2-6/M82	1.395	0.505
3-2/M82	1.11259	0.84
4-1-1/M82	N/A	N/A
4-1/M82	0.99117
4-3-2/M82	1.23546	1
4-3/M82	1.64795	1
5-3/M82	1.16711	0.447
6-2/M82	1.05508
6-3/M82	0.91382
7-1/M82	1.00374
7-2/M82	N/A	N/A
9-3-2/M82	1.21844

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.01187	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.59473	0.418
IL12-4/WTpooled	0.97381	1
IL1-4/WTpooled	0.78504	0.402
WT/WTpooled	1.00616	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	0.92971	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9442	1
DC3000/delta hrp 6h	1.0028	0.95
DC3000/delta hrp 12h	0.99799	1
DC3000/delta hrp 24h	0.96542	0.769

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9258
DC3000 delta B/DC3000 delta AB	1.40598

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96829	1
Exp 36h	1.00745	1
Exp 60h	0.87705	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96906	1
Var 0h	0.50556	1
Var 12h I row2-row1	0.98348	0.856
Var 12h NI row2-row1	1.12805	0.649
Var 36h I row2-row1	1.00502	1
Var 36h NI row2-row1	0.94554	0.791
Var 60h I row2-row1	0.87879	0.306
Var 60h NI row2-row1	1.03941	1
Time course 0hI-0hNI	0.96513	0.817
Time course 12hI-12hNI	0.98717	0.94
Time course 36hI-36hNI	0.9801	0.569
Time course 60hI-60hNI	0.9208	0.319

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)	0.98186	0.428
transgenic ySAMdc/azygous control (breaker)	1.1698	1
transgenic ySAMdc/azygous control (red)	1.11823	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02783	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21004	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.52102	0.088
Manapal/WT (break)	1.26525	0.381
Manapal/WT (red)	1.4294	0.413