Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.8.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95312	0.671
27DAP/17DAP	2.17079	0.145
39DAP/27DAP	0.9764	0.7
41DAP/39DAP	0.92334	0.675
42DAP/41DAP	1.23311	0.608
43DAP/42DAP	1.13151	1
47DAP/43DAP	1.1438	0.926
52DAP/47DAP	0.98371	0.889
57DAP/52DAP	0.98416	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98616	0.616
17DAP/reference	0.97217	0.597
27DAP/reference	1.01411	1
39DAP/reference	1.00194	0.975
41DAP/reference	0.89632	0.201
42DAP/reference	0.91844	0.085
43DAP/reference	0.84987	0.02
47DAP/reference	0.86814	0.09
52DAP/reference	0.78246	0.079
57DAP/reference	1.00055	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23781	0.379
27DAP/17DAP	1.50553	0.045
39DAP/27DAP	1.83248	0.064
41DAP/39DAP	0.69754	0.117
42DAP/41DAP	1.32142	0.004
43DAP/42DAP	1.10499	0.273
47DAP/43DAP	0.8805	0.239
52DAP/47DAP	1.13552	0.649
57DAP/52DAP	0.88934	0.405
57DAP/7DAP	1.67048	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96045	0.495
17DAP/reference	1.4465	0.399
27DAP/reference	1.24883	0.551
39DAP/reference	1.11277	0.252
41DAP/reference	1.03074	0.848
42DAP/reference	0.94211	0.32
43DAP/reference	1.06316	1
47DAP/reference	1.04998	1
52DAP/reference	1.34177	0.081
57DAP/reference	0.95806	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94763	0.518
17DAP/reference	0.72797	0.017
27DAP/reference	0.9409	0.34
39DAP/reference	0.80044	0.041
41DAP/reference	0.82652	0.061
42DAP/reference	0.88276	0.237
43DAP/reference	0.92395	0.378
47DAP/reference	0.85146	0.145
52DAP/reference	0.80622	0.031
57DAP/reference	0.99723	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93848	0.526
17DAP/reference	0.97234	0.624
27DAP/reference	1.02603	0.805
39DAP/reference	1.01317	1
41DAP/reference	1.01411	0.754
42DAP/reference	0.98413	0.816
43DAP/reference	0.91798	0.398
47DAP/reference	0.96502	0.434
52DAP/reference	1.15985	0.674
57DAP/reference	1.05297	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98142	1
26DAP/20DAP	1.21047	0.238
34DAP/26DAP	1.45828	0.542
51DAP/34DAP	2.42266	0.031
52DAP/51DAP	0.95742	1
53DAP/52DAP	1.59132	0.044
55DAP/53DAP	0.79995	0.14
57DAP/55DAP	0.74203	0.249
62DAP/57DAP	0.85369	0.466
68DAP/62DAP	1.37472	0.646
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.42592	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70746	0.221
Mature Green Tomato/Ripe Tomato	0.9566	0.715
Immature Eggplant/Mature Eggplant	4.28117	0.05
Ripe Pepper/Ripe Tomato	4.41554	0.256
Mature Eggplant/Ripe Tomato	2.07628	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78083
1-1-2/M82	1.0665	1
12-2/M82	1.62007	0.519
12-4/M82	0.95399	1
1-3/M82	1.67556	1
2-1-1/M82	0.98693	1
2-1/M82	0.88704	1
2-6/M82	0.86376	1
3-2/M82	1.43627
4-1-1/M82	0.89131
4-1/M82	0.78896	1
4-3-2/M82	1.01572	1
4-3/M82	0.84565	0.72
5-3/M82	1.01825	1
6-2/M82	1.30841
6-3/M82	1.17693	1
7-1/M82	1.12445	1
7-2/M82	0.97281	1
9-3-2/M82	1.38768	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.91631	1
IL7-5/WTpooled	2.14835
IL7-3/WTpooled	1.11865	1
IL12-4/WTpooled	0.8237	0.71
IL1-4/WTpooled	1.07431	1
WT/WTpooled	0.93406	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	1.07549	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8362
DC3000/delta hrp 6h	1.08541	1
DC3000/delta hrp 12h	1.17719	1
DC3000/delta hrp 24h	3.44832	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.9565	0.042
DC3000 delta B/DC3000 delta AB	1.61248	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.48063	0.489
Exp 60h	1.33534	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9784	1
Var 0h	0.97903	1
Var 12h I row2-row1	1.12059	0.443
Var 12h NI row2-row1	0.99004	1
Var 36h I row2-row1	0.94532	1
Var 36h NI row2-row1	1.14394	1
Var 60h I row2-row1	0.7971	0.285
Var 60h NI row2-row1	1.17786	0.904
Time course 0hI-0hNI	1.0407	0.852
Time course 12hI-12hNI	0.96653	0.759
Time course 36hI-36hNI	1.00995	0.798
Time course 60hI-60hNI	1.44526	0.017

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)	0.93204	0.377
transgenic ySAMdc/azygous control (breaker)	1.11084	0.178
transgenic ySAMdc/azygous control (red)	0.99616	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28191	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75517	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94233	1
Manapal/WT (break)	1.24165	1
Manapal/WT (red)	0.74469	0.181