Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.20.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7569	0.221
27DAP/17DAP	1.26931	0.755
39DAP/27DAP	1.00304	0.749
41DAP/39DAP	1.24556	0.108
42DAP/41DAP	1.183	0.856
43DAP/42DAP	1.0527	1
47DAP/43DAP	1.15029	0.269
52DAP/47DAP	1.08339	0.989
57DAP/52DAP	1.02686	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96688	0.578
17DAP/reference	1.14103	0.083
27DAP/reference	1.07145	0.735
39DAP/reference	1.07013	0.722
41DAP/reference	0.92706	0.154
42DAP/reference	0.92902	0.107
43DAP/reference	1.00466	0.924
47DAP/reference	0.89283	0.322
52DAP/reference	0.81512	0.244
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81109	0.201
27DAP/17DAP	N/A	N/A
39DAP/27DAP	1.19409	0.465
41DAP/39DAP	0.67381	0.347
42DAP/41DAP	0.99611	0.721
43DAP/42DAP	1.05449	1
47DAP/43DAP	0.93769	0.833
52DAP/47DAP	1.17382	0.589
57DAP/52DAP	1.15508	0.657
57DAP/7DAP	0.98353	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23673	0.11
17DAP/reference	1.39327	0.013
27DAP/reference	1.5655	0.008
39DAP/reference	2.08237	0.005
41DAP/reference	1.86952	0.015
42DAP/reference	2.26969	0.006
43DAP/reference	1.91498	0.007
47DAP/reference	1.19123	0.468
52DAP/reference	1.48612	0.036
57DAP/reference	1.8039	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03853	0.951
17DAP/reference	0.99688	0.642
27DAP/reference	0.90757	0.366
39DAP/reference	0.88329	0.189
41DAP/reference	0.94061	0.291
42DAP/reference	1.18461	1
43DAP/reference	1.19147	0.997
47DAP/reference	0.90439	0.227
52DAP/reference	0.91121	0.171
57DAP/reference	1.06458	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11928	0.303
17DAP/reference	0.94531	0.519
27DAP/reference	1.34709	0.021
39DAP/reference	1.16004	0.043
41DAP/reference	1.13876	0.343
42DAP/reference	1.40512	0.06
43DAP/reference	1.19183	0.026
47DAP/reference	0.90657	0.191
52DAP/reference	1.83637	0.094
57DAP/reference	1.3502	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30523	0.966
26DAP/20DAP	1.6892
34DAP/26DAP	1.35445	0.542
51DAP/34DAP	0.44405
52DAP/51DAP	1.03017	1
53DAP/52DAP	1.12301	0.935
55DAP/53DAP	1.09327	0.908
57DAP/55DAP	1.19009	0.986
62DAP/57DAP	1.11607	0.515
68DAP/62DAP	0.97096	0.863
68DAP/14DAP	0.97993	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.54636	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.63455	0.02
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.48202
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.90716
12-2/M82	N/A	N/A
12-4/M82	0.88116
1-3/M82	N/A	N/A
2-1-1/M82	1.51654
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	1.14633	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	0.89078
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07501
IL2-6/WTpooled	1.46597
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.08191
WT/WTpooled	1.00959	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	0.4502

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09523	0.921
DC3000/delta hrp 6h	1.1196	1
DC3000/delta hrp 12h	1.09299	1
DC3000/delta hrp 24h	0.9077	0.246

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	3.39292

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.38147	0.693
Exp 60h	1.55417	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89505
Var 0h	N/A	N/A
Var 12h I row2-row1	0.95437	0.948
Var 12h NI row2-row1	0.90718	0.906
Var 36h I row2-row1	1.44123
Var 36h NI row2-row1	2.40576	1
Var 60h I row2-row1	1.09894
Var 60h NI row2-row1	2.11384	1
Time course 0hI-0hNI	0.89125	0.555
Time course 12hI-12hNI	0.94049	0.725
Time course 36hI-36hNI	0.82326	0.312
Time course 60hI-60hNI	0.66105	0.026

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)	1.31027	0.312
transgenic ySAMdc/azygous control (breaker)	0.56768	0.134
transgenic ySAMdc/azygous control (red)	0.97275	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08744	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06095	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11962	0.307
Manapal/WT (break)	1.12367	1
Manapal/WT (red)	0.95477	0.728