Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.9.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.51663	0.153
27DAP/17DAP	1.08397	0.895
39DAP/27DAP	1.19361	0.85
41DAP/39DAP	0.66297	0.171
42DAP/41DAP	1.20008	0.916
43DAP/42DAP	0.90676	0.864
47DAP/43DAP	0.87873	0.576
52DAP/47DAP	1.21463	0.832
57DAP/52DAP	0.80776	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07329	0.11
17DAP/reference	1.11974	0.037
27DAP/reference	1.05528	0.339
39DAP/reference	1.0731	0.047
41DAP/reference	1.15283	0.015
42DAP/reference	1.05063	0.431
43DAP/reference	1.08336	0.133
47DAP/reference	1.06073	0.478
52DAP/reference	0.9938	0.636
57DAP/reference	0.89027	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07026	0.642
27DAP/17DAP	0.99874	1
39DAP/27DAP	1.15932	0.214
41DAP/39DAP	1.00936	0.921
42DAP/41DAP	0.96823	0.721
43DAP/42DAP	1.17034	0.056
47DAP/43DAP	1.19467	0.161
52DAP/47DAP	0.96858	0.899
57DAP/52DAP	0.93788	0.507
57DAP/7DAP	1.05275	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98536	0.613
17DAP/reference	0.92829	0.253
27DAP/reference	1.28861	0.009
39DAP/reference	1.16018	0.133
41DAP/reference	1.06117	0.791
42DAP/reference	1.29534	0.1
43DAP/reference	1.19554	0.074
47DAP/reference	1.18732	0.235
52DAP/reference	1.22603	0.025
57DAP/reference	1.08834	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.068	0.507
17DAP/reference	1.20694	0.124
27DAP/reference	1.1772	0.111
39DAP/reference	1.12135	0.355
41DAP/reference	1.03391	1
42DAP/reference	1.06286	0.621
43DAP/reference	1.04694	0.562
47DAP/reference	0.9659	0.319
52DAP/reference	1.15622	0.029
57DAP/reference	1.32133	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77727	0.035
17DAP/reference	0.87626	0.105
27DAP/reference	0.989	0.691
39DAP/reference	1.14674	0.075
41DAP/reference	0.89255	0.293
42DAP/reference	0.94943	0.552
43DAP/reference	0.96727	0.348
47DAP/reference	0.93336	0.183
52DAP/reference	1.02948	0.876
57DAP/reference	0.71985	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01728	0.966
26DAP/20DAP	0.89129	0.512
34DAP/26DAP	0.98122	0.972
51DAP/34DAP	0.98834	0.893
52DAP/51DAP	0.96351	1
53DAP/52DAP	1.29197	0.24
55DAP/53DAP	1.04819	0.733
57DAP/55DAP	0.98791	0.909
62DAP/57DAP	0.97498	0.871
68DAP/62DAP	0.9024	0.429
68DAP/14DAP	0.87069	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32939	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.05526	0.05
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.44356	0.092
Ripe Pepper/Ripe Tomato	0.84789	1
Mature Eggplant/Ripe Tomato	0.41411	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.58768
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.48216
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.58246
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	3.30823
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.32001
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02522	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.91515	1
IL12-4/WTpooled	1.02659	0.737
IL1-4/WTpooled	0.97424
WT/WTpooled	1.02744	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	1.21241	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99617	1
DC3000/delta hrp 6h	0.91518	0.95
DC3000/delta hrp 12h	1.15939	1
DC3000/delta hrp 24h	0.8405	0.145

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04432	1
DC3000 delta B/DC3000 delta AB	1.01919	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84927	0.213
Exp 36h	1.01868	1
Exp 60h	0.99736	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0004	1
Var 0h	1.07929	0.98
Var 12h I row2-row1	1.30208	0.283
Var 12h NI row2-row1	0.89699	0.494
Var 36h I row2-row1	1.06276	1
Var 36h NI row2-row1	1.4631	1
Var 60h I row2-row1	1.64625	1
Var 60h NI row2-row1	1.23684	0.904
Time course 0hI-0hNI	1.13365	0.377
Time course 12hI-12hNI	0.98286	0.897
Time course 36hI-36hNI	0.95936	0.317
Time course 60hI-60hNI	1.12411	0.053

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)	0.8882	0.338
transgenic ySAMdc/azygous control (breaker)	0.78277	0.173
transgenic ySAMdc/azygous control (red)	0.7784	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00003	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.4715	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92673	1
Manapal/WT (break)	0.75465	0.333
Manapal/WT (red)	0.85925	0.229