Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.7.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.9916	0.157
27DAP/17DAP	1.09623	0.859
39DAP/27DAP	1.1842	0.768
41DAP/39DAP	1.28982	0.78
42DAP/41DAP	1.35575	0.256
43DAP/42DAP	1.04204	0.948
47DAP/43DAP	1.1751	0.542
52DAP/47DAP	0.98155	0.906
57DAP/52DAP	0.72046	0.591

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86858	0.106
17DAP/reference	0.86867	0.18
27DAP/reference	0.8583	0.059
39DAP/reference	1.01803	0.871
41DAP/reference	0.93844	0.434
42DAP/reference	1.20449	0.035
43DAP/reference	1.22932	0.008
47DAP/reference	1.24737	0.081
52DAP/reference	0.75242	0.013
57DAP/reference	0.88449	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13826	0.91
27DAP/17DAP	1.35023	0.383
39DAP/27DAP	0.90405	0.405
41DAP/39DAP	0.96738	0.973
42DAP/41DAP	0.96611	0.717
43DAP/42DAP	1.46674	0.134
47DAP/43DAP	0.90352	0.325
52DAP/47DAP	1.19182	0.432
57DAP/52DAP	0.76065	0.091
57DAP/7DAP	1.66482	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7282	0.091
17DAP/reference	0.81079	0.049
27DAP/reference	0.87437	0.033
39DAP/reference	1.20609	0.018
41DAP/reference	1.08685	0.232
42DAP/reference	1.05832	0.889
43DAP/reference	0.9439	0.321
47DAP/reference	1.7573	0.018
52DAP/reference	1.15026	0.183
57DAP/reference	0.85692	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89901	0.277
17DAP/reference	0.86987	0.124
27DAP/reference	1.15054	0.283
39DAP/reference	0.93774	0.257
41DAP/reference	1.11665	0.327
42DAP/reference	0.91862	0.081
43DAP/reference	1.16884	0.854
47DAP/reference	1.20722	0.067
52DAP/reference	0.73621	0.086
57DAP/reference	0.97355	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67825	0.028
17DAP/reference	0.84426	0.231
27DAP/reference	0.92166	0.357
39DAP/reference	0.84466	0.046
41DAP/reference	0.90756	0.293
42DAP/reference	0.96817	0.671
43DAP/reference	1.21228	0.164
47DAP/reference	1.51868	0.018
52DAP/reference	1.03113	0.854
57DAP/reference	0.93721	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13439	0.966
26DAP/20DAP	0.92811	1
34DAP/26DAP	4.22605	1
51DAP/34DAP	1.11817	0.883
52DAP/51DAP	1.08273	1
53DAP/52DAP	1.36148	0.149
55DAP/53DAP	1.71831	0.382
57DAP/55DAP	1.12964	0.424
62DAP/57DAP	1.12013	0.902
68DAP/62DAP	0.92197
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.49684	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.92724	0.527
Mature Green Tomato/Ripe Tomato	1.4497	0.149
Immature Eggplant/Mature Eggplant	2.00546	0.05
Ripe Pepper/Ripe Tomato	0.68874	0.224
Mature Eggplant/Ripe Tomato	0.66375	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14247	0.742
1-1-2/M82	1.2556
12-2/M82	1.08643	1
12-4/M82	1.2659	1
1-3/M82	0.66427	0.378
2-1-1/M82	0.95769
2-1/M82	N/A	N/A
2-6/M82	1.3857	0.374
3-2/M82	0.59471	1
4-1-1/M82	0.94972	1
4-1/M82	1.84371	0.512
4-3-2/M82	0.99279	1
4-3/M82	1.18863	1
5-3/M82	0.93303	0.49
6-2/M82	0.90307
6-3/M82	1.02851	1
7-1/M82	1.07043	1
7-2/M82	0.92643	0.469
9-3-2/M82	1.67031	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.19749	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.67319	1
IL12-4/WTpooled	1.04607	0.891
IL1-4/WTpooled	1.32379
WT/WTpooled	0.93528	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	0.80397	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03464	0.921
DC3000/delta hrp 6h	1.15116	1
DC3000/delta hrp 12h	0.99417	1
DC3000/delta hrp 24h	1.05641	0.779

Experiment: DC3000 effector mutants

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

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11987	1
Exp 36h	1.14209	1
Exp 60h	1.4229	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06508	1
Var 0h	0.5036	0.98
Var 12h I row2-row1	1.05524	0.692
Var 12h NI row2-row1	0.97296	0.82
Var 36h I row2-row1	0.89094	0.575
Var 36h NI row2-row1	1.06611	1
Var 60h I row2-row1	1.36401	1
Var 60h NI row2-row1	1.02369	1
Time course 0hI-0hNI	0.96276	0.795
Time course 12hI-12hNI	1.12363	0.403
Time course 36hI-36hNI	0.85006	0.066
Time course 60hI-60hNI	0.62966	0.081

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)	0.72634	0.291
transgenic ySAMdc/azygous control (breaker)	0.91606	0.49
transgenic ySAMdc/azygous control (red)	1.00474	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12506	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91505	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02125	1
Manapal/WT (break)	0.95859	1
Manapal/WT (red)	1.23814	0.413