Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.20.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96715	0.779
27DAP/17DAP	1.06126	0.99
39DAP/27DAP	1.28753	0.533
41DAP/39DAP	1.23838	0.765
42DAP/41DAP	1.12795	1
43DAP/42DAP	0.97946	0.925
47DAP/43DAP	1.45839	0.502
52DAP/47DAP	0.93184	0.8
57DAP/52DAP	1.10434	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03135	0.71
17DAP/reference	1.07283	0.018
27DAP/reference	1.04513	0.271
39DAP/reference	1.01466	0.474
41DAP/reference	0.95697	0.542
42DAP/reference	0.95714	0.085
43DAP/reference	0.97907	0.675
47DAP/reference	0.92002	0.071
52DAP/reference	0.86175	0.105
57DAP/reference	0.88562	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94674	0.336
27DAP/17DAP	1.03623	0.872
39DAP/27DAP	1.07961	0.532
41DAP/39DAP	1.03976	0.868
42DAP/41DAP	1.03286	0.795
43DAP/42DAP	1.0145	0.664
47DAP/43DAP	1.00405	0.973
52DAP/47DAP	1.00337	1
57DAP/52DAP	1.03999	0.763
57DAP/7DAP	1.0964	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37748	0.06
17DAP/reference	1.44329	0.016
27DAP/reference	1.32954	0.008
39DAP/reference	1.52823	0.007
41DAP/reference	1.27973	0.019
42DAP/reference	1.34238	0.012
43DAP/reference	1.50753	0.006
47DAP/reference	1.2048	0.353
52DAP/reference	1.81873	0.008
57DAP/reference	1.58607	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99855	0.951
17DAP/reference	0.93973	0.201
27DAP/reference	0.85156	0.111
39DAP/reference	0.91189	0.178
41DAP/reference	0.94288	0.277
42DAP/reference	0.90642	0.212
43DAP/reference	0.89787	0.25
47DAP/reference	1.03027	0.675
52DAP/reference	0.9384	0.101
57DAP/reference	0.96449	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27351	0.03
17DAP/reference	1.05035	0.804
27DAP/reference	1.28456	0.043
39DAP/reference	1.27117	0.02
41DAP/reference	1.23245	0.104
42DAP/reference	1.07466	0.759
43DAP/reference	1.04905	0.827
47DAP/reference	0.97222	0.452
52DAP/reference	1.36432	0.198
57DAP/reference	0.82817	0.221

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02393	0.966
26DAP/20DAP	0.93714	1
34DAP/26DAP	0.9637	0.861
51DAP/34DAP	0.92649	0.482
52DAP/51DAP	0.97871	1
53DAP/52DAP	0.9761	0.868
55DAP/53DAP	0.90085	0.478
57DAP/55DAP	1.08048	0.543
62DAP/57DAP	0.98677	0.994
68DAP/62DAP	0.83521	0.609
68DAP/14DAP	1.17594	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85992	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.80267
Mature Green Tomato/Ripe Tomato	0.87948
Immature Eggplant/Mature Eggplant	1.35714	0.379
Ripe Pepper/Ripe Tomato	1.23221
Mature Eggplant/Ripe Tomato	1.33145

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95646	0.944
1-1-2/M82	0.8639	0.804
12-2/M82	1.03183	1
12-4/M82	1.57349	1
1-3/M82	0.83691	0.378
2-1-1/M82	1.04552
2-1/M82	N/A	N/A
2-6/M82	1.27698	0.505
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.98183
4-3-2/M82	0.81564
4-3/M82	0.75963	0.72
5-3/M82	0.91693	0.395
6-2/M82	1.00843	1
6-3/M82	0.88429
7-1/M82	1.13525
7-2/M82	1.06416	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99456	1
IL2-6/WTpooled	0.50492	0.473
IL7-5/WTpooled	0.81473	1
IL7-3/WTpooled	1.16814	1
IL12-4/WTpooled	0.85801	0.71
IL1-4/WTpooled	1.13575	0.426
WT/WTpooled	1.08256	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	1.73292	0.117

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96872	1
DC3000/delta hrp 6h	1.25722	1
DC3000/delta hrp 12h	1.09456	1
DC3000/delta hrp 24h	1.14392	0.397

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03958	0.313
DC3000 delta B/DC3000 delta AB	1.02852	0.665

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08695	1
Exp 36h	1.14526	0.693
Exp 60h	1.19816	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.72002	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.12477	0.296
Var 12h NI row2-row1	0.95122	0.713
Var 36h I row2-row1	0.86797	0.805
Var 36h NI row2-row1	1.07777	1
Var 60h I row2-row1	1.15315	0.562
Var 60h NI row2-row1	1.00653	1
Time course 0hI-0hNI	1.08847	0.799
Time course 12hI-12hNI	1.07225	0.714
Time course 36hI-36hNI	0.99537	0.742
Time course 60hI-60hNI	1.2473	0.009

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)	2.10861	0.212
transgenic ySAMdc/azygous control (breaker)	1.45207	0.178
transgenic ySAMdc/azygous control (red)	1.10377	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98093	0.343

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87068	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.67772	1
Manapal/WT (break)	0.95928	1
Manapal/WT (red)	0.83104	0.424