Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.19.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06516	0.964
27DAP/17DAP	0.89411	0.753
39DAP/27DAP	0.97203	0.749
41DAP/39DAP	0.75357	0.212
42DAP/41DAP	1.05636	0.978
43DAP/42DAP	1.06387	1
47DAP/43DAP	0.86091	0.562
52DAP/47DAP	1.06085	0.902
57DAP/52DAP	1.20397	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00706	0.616
17DAP/reference	0.83682	0.18
27DAP/reference	0.91816	0.223
39DAP/reference	0.73749	0.146
41DAP/reference	0.7472	0.267
42DAP/reference	0.82432	0.05
43DAP/reference	0.75601	0.013
47DAP/reference	1.07682	1
52DAP/reference	1.21349	0.038
57DAP/reference	0.66678	0.277

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11958	0.482
27DAP/17DAP	1.05711	0.768
39DAP/27DAP	0.83506	0.05
41DAP/39DAP	1.28994	0.774
42DAP/41DAP	1.09177	0.687
43DAP/42DAP	0.8329	0.022
47DAP/43DAP	1.06471	0.758
52DAP/47DAP	0.88395	0.222
57DAP/52DAP	1.08174	0.558
57DAP/7DAP	1.03554	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0218	1
17DAP/reference	0.93436	0.22
27DAP/reference	0.99762	0.698
39DAP/reference	1.07955	0.705
41DAP/reference	0.8623	0.094
42DAP/reference	0.84802	0.178
43DAP/reference	0.92127	0.183
47DAP/reference	0.95913	0.504
52DAP/reference	1.13519	0.599
57DAP/reference	0.94553	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87607	0.318
17DAP/reference	0.80813	0.08
27DAP/reference	0.94266	0.327
39DAP/reference	1.0649	0.705
41DAP/reference	1.16935	0.255
42DAP/reference	0.95065	0.108
43DAP/reference	0.79111	0.049
47DAP/reference	0.80671	0.013
52DAP/reference	1.05013	0.838
57DAP/reference	0.79136	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92167	0.268
17DAP/reference	1.02465	1
27DAP/reference	0.98175	0.624
39DAP/reference	0.90742	0.043
41DAP/reference	0.96728	0.56
42DAP/reference	1.01628	1
43DAP/reference	0.95203	0.468
47DAP/reference	1.02614	0.646
52DAP/reference	0.68636	0.063
57DAP/reference	1.08806	0.56

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.55142	0.752
26DAP/20DAP	1.21771	0.259
34DAP/26DAP	1.01747	1
51DAP/34DAP	0.89507	0.369
52DAP/51DAP	1.05643	0.638
53DAP/52DAP	1.00882	0.961
55DAP/53DAP	1.00357	0.908
57DAP/55DAP	1.01017	0.914
62DAP/57DAP	1.13106	0.622
68DAP/62DAP	1.99412	0.05
68DAP/14DAP	2.13747	0.038

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.83086	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.68347	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95669
1-1-2/M82	0.89698	1
12-2/M82	0.91941	0.862
12-4/M82	1.05087
1-3/M82	N/A	N/A
2-1-1/M82	0.42078	0.784
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.85091
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	0.92364	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.90931	0.881
9-3-2/M82	1.34296

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75634	0.243
IL2-6/WTpooled	1.24581	0.46
IL7-5/WTpooled	0.65958	0.559
IL7-3/WTpooled	1.18154	1
IL12-4/WTpooled	1.0901	0.737
IL1-4/WTpooled	0.8322	0.562
WT/WTpooled	1.00807	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	1.00691	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97602	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.98932	1
DC3000/delta hrp 24h	0.96801	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84682	0.052
DC3000 delta B/DC3000 delta AB	0.89027	0.142

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98283	1
Var 0h	1.75275	0.98
Var 12h I row2-row1	0.99376	1
Var 12h NI row2-row1	1.06362	1
Var 36h I row2-row1	1.17981	0.601
Var 36h NI row2-row1	1.02331	1
Var 60h I row2-row1	0.8452	0.832
Var 60h NI row2-row1	0.9228	0.866
Time course 0hI-0hNI	0.95082	0.711
Time course 12hI-12hNI	1.03906	0.714
Time course 36hI-36hNI	1.06191	0.401
Time course 60hI-60hNI	0.68947	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)	1.05857	0.612
transgenic ySAMdc/azygous control (breaker)	1.20142	0.248
transgenic ySAMdc/azygous control (red)	1.07353	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0191	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02345	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.93269	0.242