Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.14.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0341	0.893
27DAP/17DAP	1.0168	0.93
39DAP/27DAP	0.95382	0.663
41DAP/39DAP	1.32311	0.258
42DAP/41DAP	0.88121	1
43DAP/42DAP	0.95002	0.841
47DAP/43DAP	1.05303	0.776
52DAP/47DAP	1.28236	0.424
57DAP/52DAP	0.96817	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05544	0.334
17DAP/reference	1.00618	0.843
27DAP/reference	1.00904	0.934
39DAP/reference	1.01193	0.722
41DAP/reference	1.00692	0.963
42DAP/reference	1.04328	0.13
43DAP/reference	0.97437	0.464
47DAP/reference	0.98964	0.503
52DAP/reference	1.05574	0.524
57DAP/reference	1.01953	0.927

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03032	0.675
27DAP/17DAP	1.02294	0.938
39DAP/27DAP	0.96184	0.732
41DAP/39DAP	0.90801	0.276
42DAP/41DAP	1.04676	0.694
43DAP/42DAP	1.00257	1
47DAP/43DAP	0.98139	0.919
52DAP/47DAP	0.99096	0.935
57DAP/52DAP	1.01594	0.957
57DAP/7DAP	1.07979	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96626	0.203
17DAP/reference	1.01736
27DAP/reference	0.95791	0.215
39DAP/reference	0.97843	0.23
41DAP/reference	0.97576	0.311
42DAP/reference	1.05043	0.076
43DAP/reference	1.02833	0.325
47DAP/reference	0.94454	0.222
52DAP/reference	0.92772	0.106
57DAP/reference	0.98089	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9835	0.72
17DAP/reference	1.03262	0.437
27DAP/reference	1.06904	0.412
39DAP/reference	0.98489	0.469
41DAP/reference	0.98356	0.493
42DAP/reference	1.00676	1
43DAP/reference	1.05359	0.401
47DAP/reference	1.00324	1
52DAP/reference	0.98316	0.327
57DAP/reference	0.99953	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95908	0.23
17DAP/reference	0.98852	0.668
27DAP/reference	0.97629	0.337
39DAP/reference	1.03404	0.39
41DAP/reference	0.9618	0.209
42DAP/reference	0.9581	0.134
43DAP/reference	0.99569	0.767
47DAP/reference	0.91262	0.089
52DAP/reference	0.97326	0.596
57DAP/reference	0.92707	0.152

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97428	1
26DAP/20DAP	0.98326	1
34DAP/26DAP	0.9423	0.488
51DAP/34DAP	0.92586	0.385
52DAP/51DAP	0.99597	1
53DAP/52DAP	0.98873	0.938
55DAP/53DAP	0.94264	0.632
57DAP/55DAP	1.01819	0.997
62DAP/57DAP	1.34923	0.515
68DAP/62DAP	1.07499	0.689
68DAP/14DAP	1.08198	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96917	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.38905	0.058
Mature Green Tomato/Ripe Tomato	1.41221	0.022
Immature Eggplant/Mature Eggplant	0.37554	0.125
Ripe Pepper/Ripe Tomato	2.66005	1
Mature Eggplant/Ripe Tomato	3.77394	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99454	1
1-1-2/M82	0.86586	1
12-2/M82	1.00965	1
12-4/M82	1.0056	1
1-3/M82	0.78997	0.441
2-1-1/M82	1.174	0.764
2-1/M82	N/A	N/A
2-6/M82	1.15336	0.505
3-2/M82	0.94263
4-1-1/M82	N/A	N/A
4-1/M82	1.08162
4-3-2/M82	1.00759	1
4-3/M82	N/A	N/A
5-3/M82	0.99825	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.0312	1
9-3-2/M82	0.89072	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.38932	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.266	0.362
IL12-4/WTpooled	1.18589	0.553
IL1-4/WTpooled	1.41803	0.426
WT/WTpooled	0.95822

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	0.8877	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92809	1
DC3000/delta hrp 6h	0.97153	0.95
DC3000/delta hrp 12h	0.94276	1
DC3000/delta hrp 24h	0.90438	0.371

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13438	0.044
DC3000 delta B/DC3000 delta AB	1.03263	0.614

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02954	1
Exp 36h	1.0411	1
Exp 60h	1.00777	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99816	1
Var 0h	0.52699	1
Var 12h I row2-row1	0.96555	0.77
Var 12h NI row2-row1	0.91846	0.546
Var 36h I row2-row1	0.97687	1
Var 36h NI row2-row1	1.11908	0.482
Var 60h I row2-row1	1.09504	1
Var 60h NI row2-row1	0.94703	0.932
Time course 0hI-0hNI	1.06551	0.603
Time course 12hI-12hNI	0.98036	0.814
Time course 36hI-36hNI	0.95803	0.306
Time course 60hI-60hNI	0.82602	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)	0.93274	0.662
transgenic ySAMdc/azygous control (breaker)	1.157	1
transgenic ySAMdc/azygous control (red)	1.22082	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99117	0.418

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	5.79629	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08542	1
Manapal/WT (break)	1.04751	1
Manapal/WT (red)	3.5785	0.133