Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.12.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85483	0.265
27DAP/17DAP	1.14562	0.872
39DAP/27DAP	1.23126	0.782
41DAP/39DAP	0.6297	0.068
42DAP/41DAP	0.7805	0.397
43DAP/42DAP	0.72239	0.434
47DAP/43DAP	1.40299	0.448
52DAP/47DAP	1.6344	0.371
57DAP/52DAP	0.76245	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75866	0.009
17DAP/reference	0.85369	0.069
27DAP/reference	0.8545	0.027
39DAP/reference	1.21863	0.101
41DAP/reference	1.04577	0.808
42DAP/reference	1.37839	0.001
43DAP/reference	0.83498	0.061
47DAP/reference	1.11131	0.593
52DAP/reference	1.01682	1
57DAP/reference	1.05904	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83655	0.17
27DAP/17DAP	1.0068	1
39DAP/27DAP	0.95496	0.703
41DAP/39DAP	1.62195	0.065
42DAP/41DAP	0.64329	0.009
43DAP/42DAP	1.00461	1
47DAP/43DAP	1.00822	0.919
52DAP/47DAP	0.98292	0.917
57DAP/52DAP	1.10222	0.65
57DAP/7DAP	0.54253	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26409	0.524
17DAP/reference	1.18397	0.035
27DAP/reference	1.25153	0.023
39DAP/reference	0.91674	0.23
41DAP/reference	1.16877	0.215
42DAP/reference	1.12367	0.308
43DAP/reference	1.34763	0.012
47DAP/reference	1.571	0.165
52DAP/reference	1.82437	0.007
57DAP/reference	1.5381	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66271	0.037
17DAP/reference	2.12681	0.009
27DAP/reference	1.62592	0.023
39DAP/reference	1.39938	0.17
41DAP/reference	1.17087	0.814
42DAP/reference	2.04395	0.008
43DAP/reference	1.71912	0.034
47DAP/reference	1.99744	0.008
52DAP/reference	1.46318	0.038
57DAP/reference	1.88963	0.031

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0937	0.397
17DAP/reference	1.17837	0.602
27DAP/reference	1.3584	0.025
39DAP/reference	1.26898	0.015
41DAP/reference	1.69134	0.145
42DAP/reference	1.656	0.057
43DAP/reference	1.72648	0.254
47DAP/reference	1.96091	0.011
52DAP/reference	1.38415	0.09
57DAP/reference	3.60344	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.37487	0.85
26DAP/20DAP	0.73581	0.317
34DAP/26DAP	1.1234	0.819
51DAP/34DAP	0.91735	0.522
52DAP/51DAP	0.99597	1
53DAP/52DAP	0.86347	0.409
55DAP/53DAP	0.76009	0.159
57DAP/55DAP	1.10606	0.805
62DAP/57DAP	1.06265	0.8
68DAP/62DAP	1.02947	0.939
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94092	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.2689	0.058
Mature Green Tomato/Ripe Tomato	0.61341	0.018
Immature Eggplant/Mature Eggplant	0.63614	0.063
Ripe Pepper/Ripe Tomato	0.22913	0.224
Mature Eggplant/Ripe Tomato	0.9257	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26912	0.473
1-1-2/M82	0.90337	1
12-2/M82	1.16391	1
12-4/M82	0.93231	0.358
1-3/M82	1.03537	1
2-1-1/M82	N/A	N/A
2-1/M82	1.449
2-6/M82	1.1962	0.594
3-2/M82	0.95682
4-1-1/M82	1.45	0.977
4-1/M82	1.52394
4-3-2/M82	1.03649
4-3/M82	0.89015	1
5-3/M82	0.73695	0.395
6-2/M82	1.33706
6-3/M82	0.70285	0.857
7-1/M82	1.17103	1
7-2/M82	0.98899	1
9-3-2/M82	1.5352

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96491	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09766	1
IL12-4/WTpooled	1.1535	0.516
IL1-4/WTpooled	1.03247	1
WT/WTpooled	0.97029	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	1.24591	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17214	0.629
DC3000/delta hrp 6h	0.93937	0.95
DC3000/delta hrp 12h	1.13993	1
DC3000/delta hrp 24h	0.86565	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.43818
DC3000 delta B/DC3000 delta AB	0.9859	0.873

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91955	1
Exp 36h	1.20463	0.489
Exp 60h	0.93259	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03289	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.90348	0.705
Var 12h NI row2-row1	1.29094	0.281
Var 36h I row2-row1	1.20598	0.601
Var 36h NI row2-row1	0.72756	0.549
Var 60h I row2-row1	0.90174	0.832
Var 60h NI row2-row1	0.96265	1
Time course 0hI-0hNI	1.04983	0.799
Time course 12hI-12hNI	0.96915	0.827
Time course 36hI-36hNI	1.72966	0.005
Time course 60hI-60hNI	1.86403	0.008

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)	1.09679	0.541
transgenic ySAMdc/azygous control (breaker)	0.49404	0.129
transgenic ySAMdc/azygous control (red)	1.10431	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92423	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.54239	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78705	1
Manapal/WT (break)	1.07431	1
Manapal/WT (red)	0.57754	0.181