Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78527	0.226
27DAP/17DAP	1.54229	0.599
39DAP/27DAP	1.04693	0.782
41DAP/39DAP	1.11518	0.982
42DAP/41DAP	1.35978	0.767
43DAP/42DAP	0.99436	0.937
47DAP/43DAP	0.90907	0.693
52DAP/47DAP	1.11548	0.915
57DAP/52DAP	1.20406	0.873

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04254	0.587
17DAP/reference	1.01425	0.764
27DAP/reference	1.00075	0.923
39DAP/reference	1.0021	0.903
41DAP/reference	0.98288	0.341
42DAP/reference	1.02659	0.782
43DAP/reference	0.9914	0.82
47DAP/reference	0.95268	0.191
52DAP/reference	0.68959	0.042
57DAP/reference	0.80625	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05616	0.826
27DAP/17DAP	0.90775	0.446
39DAP/27DAP	1.09497	0.418
41DAP/39DAP	1.16256	0.531
42DAP/41DAP	0.90192	0.329
43DAP/42DAP	1.0382	0.664
47DAP/43DAP	1.02656	0.906
52DAP/47DAP	1.03714	0.862
57DAP/52DAP	1.02933	0.874
57DAP/7DAP	1.21099	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88462	0.076
17DAP/reference	0.93899	0.167
27DAP/reference	0.87014	0.017
39DAP/reference	1.00113	1
41DAP/reference	0.9724	0.146
42DAP/reference	0.99701	0.713
43DAP/reference	0.98083	0.351
47DAP/reference	0.88674	0.066
52DAP/reference	0.89775	0.083
57DAP/reference	1.05234	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01488	0.842
17DAP/reference	0.94408	0.214
27DAP/reference	0.85227	0.076
39DAP/reference	0.81944	0.087
41DAP/reference	0.93876	0.299
42DAP/reference	0.84874	0.073
43DAP/reference	1.0535	0.553
47DAP/reference	0.99645	0.695
52DAP/reference	0.98025	0.5
57DAP/reference	1.3673	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96647	0.526
17DAP/reference	0.9841	0.709
27DAP/reference	0.92956	0.218
39DAP/reference	0.90542	0.054
41DAP/reference	0.87199	0.025
42DAP/reference	0.77268	0.059
43DAP/reference	0.84131	0.179
47DAP/reference	1.04746	0.994
52DAP/reference	0.8782	0.247
57DAP/reference	0.72713	0.06

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04136	0.966
26DAP/20DAP	0.90744	0.512
34DAP/26DAP	1.03858	1
51DAP/34DAP	0.96581	0.785
52DAP/51DAP	1.00774	1
53DAP/52DAP	1.06958	0.688
55DAP/53DAP	1.12667	0.429
57DAP/55DAP	1.02248	1
62DAP/57DAP	1.08326	0.678
68DAP/62DAP	0.93403	0.722
68DAP/14DAP	0.99407	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84282	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.22291	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.2278	0.224
Mature Eggplant/Ripe Tomato	0.25525	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99423	1
1-1-2/M82	0.95349	1
12-2/M82	1.15649
12-4/M82	0.97019	1
1-3/M82	0.90215	0.378
2-1-1/M82	1.31348	0.375
2-1/M82	N/A	N/A
2-6/M82	1.11337	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.1354	1
4-1/M82	1.08357	1
4-3-2/M82	0.78506
4-3/M82	0.72107	1
5-3/M82	0.87975	1
6-2/M82	0.94017	1
6-3/M82	0.95577	1
7-1/M82	N/A	N/A
7-2/M82	1.06724	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90231	0.321
IL2-6/WTpooled	0.98709	1
IL7-5/WTpooled	1.09051	0.792
IL7-3/WTpooled	0.80719	0.294
IL12-4/WTpooled	0.88633	1
IL1-4/WTpooled	1.00601	1
WT/WTpooled	1.03664	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	1.05098	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06276	0.846
DC3000/delta hrp 6h	1.51785	0.19
DC3000/delta hrp 12h	1.17261	1
DC3000/delta hrp 24h	1.02969	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17738	0.121
DC3000 delta B/DC3000 delta AB	1.04641	0.571

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	2.38206	0.371
Exp 60h	1.4864	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98452	1
Var 0h	0.52631	0.936
Var 12h I row2-row1	1.04304	0.654
Var 12h NI row2-row1	0.88051	0.713
Var 36h I row2-row1	1.09455	1
Var 36h NI row2-row1	0.92952	0.706
Var 60h I row2-row1	1.19894	0.562
Var 60h NI row2-row1	1.18606	0.904
Time course 0hI-0hNI	1.16843	0.486
Time course 12hI-12hNI	1.21632	0.075
Time course 36hI-36hNI	2.03297	0.005
Time course 60hI-60hNI	1.78456	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)	1.31485	0.397
transgenic ySAMdc/azygous control (breaker)	0.26881	0.122
transgenic ySAMdc/azygous control (red)	1.14814	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99533	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.27432	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04816	1
Manapal/WT (break)	0.99105	1
Manapal/WT (red)	0.65356	0.181