Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34802	0.575
27DAP/17DAP	0.3972	0.024
39DAP/27DAP	0.8817	0.41
41DAP/39DAP	0.81534	0.389
42DAP/41DAP	0.6394	0.251
43DAP/42DAP	0.63905	0.613
47DAP/43DAP	1.70133	0.215
52DAP/47DAP	0.99558	0.907
57DAP/52DAP	0.84707	0.777

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.43656	0.034
17DAP/reference	0.18732	0.007
27DAP/reference	0.19951	0.011
39DAP/reference	0.21836	0.009
41DAP/reference	0.19664	0.008
42DAP/reference	0.26808	0.001
43DAP/reference	0.28263	0.014
47DAP/reference	0.30803	0.001
52DAP/reference	0.36956	0.023
57DAP/reference	0.48498	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.54775	0.038
27DAP/17DAP	1.16004	0.65
39DAP/27DAP	1.07199	0.603
41DAP/39DAP	0.78049	0.164
42DAP/41DAP	0.75959	0.095
43DAP/42DAP	0.87865	0.399
47DAP/43DAP	0.94456	0.787
52DAP/47DAP	1.24805	0.377
57DAP/52DAP	0.95642	0.673
57DAP/7DAP	1.77144

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.32939	0.054
17DAP/reference	0.18705	0.011
27DAP/reference	0.26849	0.01
39DAP/reference	0.14986	0.011
41DAP/reference	0.79152	0.122
42DAP/reference	0.1884	0.01
43DAP/reference	0.12593	0.008
47DAP/reference	0.18217	0.026
52DAP/reference	0.09994	0.008
57DAP/reference	0.12006	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.24313	0.005
17DAP/reference	0.16325	0.003
27DAP/reference	0.18556	0.006
39DAP/reference	0.19607	0.009
41DAP/reference	0.37455	0.012
42DAP/reference	0.3072	0.01
43DAP/reference	0.19709	0.002
47DAP/reference	0.27411	0.007
52DAP/reference	0.14534	0.003
57DAP/reference	0.16346	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37855	0.034
17DAP/reference	1.0878	0.108
27DAP/reference	0.11885	0.02
39DAP/reference	0.12497	0.006
41DAP/reference	0.17206	0.014
42DAP/reference	0.26181	0.016
43DAP/reference	0.19456	0.016
47DAP/reference	0.12743	0.004
52DAP/reference	0.16213	0.038
57DAP/reference	0.48191	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96571	1
26DAP/20DAP	0.86084	1
34DAP/26DAP	1.68427	0.304
51DAP/34DAP	1.4606	0.458
52DAP/51DAP	1.50285	0.481
53DAP/52DAP	0.69713	0.484
55DAP/53DAP	0.99125	0.864
57DAP/55DAP	1.44708	0.364
62DAP/57DAP	1.08534	1
68DAP/62DAP	1.4999	0.353
68DAP/14DAP	1.14603	0.762

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.37275	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27517
Mature Green Tomato/Ripe Tomato	5.36209	0.015
Immature Eggplant/Mature Eggplant	6.42451	0.05
Ripe Pepper/Ripe Tomato	0.39387
Mature Eggplant/Ripe Tomato	0.40345	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97859	0.961
1-1-2/M82	1.05117	1
12-2/M82	1.18527
12-4/M82	0.96119	1
1-3/M82	0.85845	0.378
2-1-1/M82	1.05463	0.764
2-1/M82	1.32592	0.345
2-6/M82	1.08286	1
3-2/M82	0.83881
4-1-1/M82	1.10398	1
4-1/M82	1.41482
4-3-2/M82	0.83631
4-3/M82	0.84862	0.72
5-3/M82	0.96179	1
6-2/M82	0.88834	1
6-3/M82	1.03681	1
7-1/M82	0.88007	1
7-2/M82	0.95144	1
9-3-2/M82	0.90447

Experiment: Tomato introgression line transcript analysis

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

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	0.77679	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98583	1
DC3000/delta hrp 6h	1.3066	1
DC3000/delta hrp 12h	0.40929	1
DC3000/delta hrp 24h	1.95093	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1444	0.16
DC3000 delta B/DC3000 delta AB	1.24506	0.149

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0229	1
Exp 36h	0.54794	0.366
Exp 60h	0.84618	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06423	1
Var 0h	1.12765	0.936
Var 12h I row2-row1	11.7709	0.506
Var 12h NI row2-row1	0.94634	0.82
Var 36h I row2-row1	0.56443	0.203
Var 36h NI row2-row1	4.12437	1
Var 60h I row2-row1	0.999	1
Var 60h NI row2-row1	0.91406	0.756
Time course 0hI-0hNI	0.84197	0.958
Time course 12hI-12hNI	0.841	0.133
Time course 36hI-36hNI	1.77713	0.799
Time course 60hI-60hNI	0.48653	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)	0.78816	0.282
transgenic ySAMdc/azygous control (breaker)	0.98087	1
transgenic ySAMdc/azygous control (red)	1.04718	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98905	0.609

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.96358	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84199	1
Manapal/WT (break)	0.32477	0.333
Manapal/WT (red)	1.76894	0.222