Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.10.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04608	0.798
27DAP/17DAP	1.02945	0.902
39DAP/27DAP	1.04602	0.894
41DAP/39DAP	0.98863	0.949
42DAP/41DAP	0.819	1
43DAP/42DAP	1.00835	0.945
47DAP/43DAP	1.02051	1
52DAP/47DAP	1.0134	0.965
57DAP/52DAP	0.99329	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99802	0.787
17DAP/reference	0.99497	0.858
27DAP/reference	0.94307	0.182
39DAP/reference	0.94622	0.424
41DAP/reference	0.992	0.814
42DAP/reference	0.98109	0.348
43DAP/reference	0.99872	0.904
47DAP/reference	0.98039	0.392
52DAP/reference	1.02994	1
57DAP/reference	1.1029	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9812	0.732
27DAP/17DAP	0.99997	1
39DAP/27DAP	0.98699	0.943
41DAP/39DAP	1.06785	0.641
42DAP/41DAP	0.95992	0.684
43DAP/42DAP	1.03024	0.212
47DAP/43DAP	0.97786	0.846
52DAP/47DAP	0.983	0.913
57DAP/52DAP	0.99264	0.869
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86222	0.06
17DAP/reference	0.97262	0.167
27DAP/reference	0.99328	0.571
39DAP/reference	0.98458	0.307
41DAP/reference	0.93907	0.122
42DAP/reference	1.02108	0.405
43DAP/reference	0.95812	0.183
47DAP/reference	0.96861	0.293
52DAP/reference	0.91605	0.213
57DAP/reference	0.9117	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04269	0.258
17DAP/reference	0.99505	0.747
27DAP/reference	0.95878	0.438
39DAP/reference	0.89288	0.102
41DAP/reference	0.89279	0.061
42DAP/reference	0.93536	0.189
43DAP/reference	0.99467	0.801
47DAP/reference	1.05607	0.164
52DAP/reference	0.9703	0.327
57DAP/reference	0.98438	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91663	0.032
17DAP/reference	0.99863	0.886
27DAP/reference	1.00676	0.903
39DAP/reference	0.99515	0.693
41DAP/reference	0.94658	0.132
42DAP/reference	0.9325	0.361
43DAP/reference	0.95213	0.15
47DAP/reference	0.96709	0.452
52DAP/reference	0.98443	0.747
57DAP/reference	0.96025	0.366

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03933	0.966
26DAP/20DAP	0.9739	1
34DAP/26DAP	1.01461	1
51DAP/34DAP	0.98752	0.901
52DAP/51DAP	1.07647
53DAP/52DAP	N/A	N/A
55DAP/53DAP	N/A	N/A
57DAP/55DAP	0.98225	0.914
62DAP/57DAP	0.9741	0.994
68DAP/62DAP	0.87281	0.406
68DAP/14DAP	1.1522	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9886	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14997	0.666
Mature Green Tomato/Ripe Tomato	0.87678	0.347
Immature Eggplant/Mature Eggplant	1.17885	0.181
Ripe Pepper/Ripe Tomato	1.47609	1
Mature Eggplant/Ripe Tomato	2.84926	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98652	0.961
1-1-2/M82	1.0132	1
12-2/M82	0.92331	0.661
12-4/M82	1.00783	1
1-3/M82	1.06771
2-1-1/M82	0.97003	0.784
2-1/M82	0.93094	1
2-6/M82	0.93763	1
3-2/M82	0.99692	1
4-1-1/M82	1.0468	1
4-1/M82	0.98241	1
4-3-2/M82	0.99768	1
4-3/M82	0.94301	0.72
5-3/M82	0.9854	1
6-2/M82	1.02217	1
6-3/M82	1.01394	1
7-1/M82	1.04058	0.925
7-2/M82	1.05943	1
9-3-2/M82	0.84755	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.24097	1
IL7-5/WTpooled	0.71265
IL7-3/WTpooled	1.11964	1
IL12-4/WTpooled	0.82278	0.566
IL1-4/WTpooled	1.62173	1
WT/WTpooled	0.99748	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	0.93957	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08502	0.875
DC3000/delta hrp 6h	1.42536	1
DC3000/delta hrp 12h	0.94553	1
DC3000/delta hrp 24h	1.01366	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08381	0.087
DC3000 delta B/DC3000 delta AB	1.14744	0.318

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06509	1
Exp 36h	1.29298	1
Exp 60h	0.88113	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04499	1
Var 0h	0.49044	0.933
Var 12h I row2-row1	1.40487	0.324
Var 12h NI row2-row1	1.01338	1
Var 36h I row2-row1	1.05043	1
Var 36h NI row2-row1	0.97682	0.645
Var 60h I row2-row1	1.22552	1
Var 60h NI row2-row1	1.12591	0.904
Time course 0hI-0hNI	1.1263	0.833
Time course 12hI-12hNI	1.03542	0.788
Time course 36hI-36hNI	1.04266	0.722
Time course 60hI-60hNI	1.39591	0.015

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)	0.91601	0.454
transgenic ySAMdc/azygous control (breaker)	1.22563	0.248
transgenic ySAMdc/azygous control (red)	1.33318	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97901	0.156

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05236	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8138	1
Manapal/WT (break)	0.87962	0.333
Manapal/WT (red)	1.10819	1