Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66906	0.134
27DAP/17DAP	0.83345	0.46
39DAP/27DAP	0.96206	0.682
41DAP/39DAP	0.97653	0.852
42DAP/41DAP	1.27375	0.507
43DAP/42DAP	1.16913	0.756
47DAP/43DAP	0.90309	0.663
52DAP/47DAP	0.93928	0.803
57DAP/52DAP	0.78565	0.605

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88087	0.085
17DAP/reference	0.76339	0.009
27DAP/reference	0.87017	0.073
39DAP/reference	0.84965	0.03
41DAP/reference	0.69879	0.008
42DAP/reference	0.94219	0.139
43DAP/reference	0.97079	0.611
47DAP/reference	1.04618	0.627
52DAP/reference	0.99873	0.636
57DAP/reference	1.41316	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26701	0.109
27DAP/17DAP	0.8186	0.339
39DAP/27DAP	0.81441	0.338
41DAP/39DAP	1.0912	0.868
42DAP/41DAP	0.96138	0.687
43DAP/42DAP	1.3645	0.017
47DAP/43DAP	1.20698	0.63
52DAP/47DAP	0.90493	0.666
57DAP/52DAP	0.9209	0.519
57DAP/7DAP	1.04985	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17994	0.129
17DAP/reference	1.16145	0.269
27DAP/reference	1.01805	0.974
39DAP/reference	1.26257	0.048
41DAP/reference	0.98367	0.565
42DAP/reference	1.18708	0.405
43DAP/reference	1.33424	0.028
47DAP/reference	1.19764	0.345
52DAP/reference	1.03172	1
57DAP/reference	0.99243	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.905	0.296
17DAP/reference	0.77257	0.017
27DAP/reference	0.89345	0.22
39DAP/reference	1.047	0.935
41DAP/reference	0.84954	0.242
42DAP/reference	0.99595	0.655
43DAP/reference	0.82361	0.206
47DAP/reference	0.8545	0.015
52DAP/reference	0.87112	0.078
57DAP/reference	0.73341	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48795	0.023
17DAP/reference	1.29283	0.865
27DAP/reference	1.32487	0.027
39DAP/reference	1.26253	0.017
41DAP/reference	1.19664	0.286
42DAP/reference	1.25273	0.053
43DAP/reference	1.36633	0.041
47DAP/reference	1.14473	0.424
52DAP/reference	1.39472	0.22
57DAP/reference	1.72467	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93341	1
26DAP/20DAP	0.91281	1
34DAP/26DAP	1.13648	1
51DAP/34DAP	1.20761	0.365
52DAP/51DAP	0.98333	1
53DAP/52DAP	1.02776	0.944
55DAP/53DAP	1.37251	0.319
57DAP/55DAP	0.95883	0.795
62DAP/57DAP	2.98782	0.622
68DAP/62DAP	1.22907	1
68DAP/14DAP	4.86584	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30922	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.60518	0.14
Mature Green Tomato/Ripe Tomato	0.7924	0.079
Immature Eggplant/Mature Eggplant	0.6694	0.067
Ripe Pepper/Ripe Tomato	1.76122	1
Mature Eggplant/Ripe Tomato	0.9887	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.64549	0.551
1-1-2/M82	1.13467	1
12-2/M82	0.90914	0.955
12-4/M82	0.7766	1
1-3/M82	N/A	N/A
2-1-1/M82	1.23362
2-1/M82	N/A	N/A
2-6/M82	1.59874	0.364
3-2/M82	0.63161
4-1-1/M82	0.56162
4-1/M82	N/A	N/A
4-3-2/M82	2.13264
4-3/M82	1.51869	1
5-3/M82	1.06108	1
6-2/M82	0.66394
6-3/M82	1.23608	1
7-1/M82	N/A	N/A
7-2/M82	0.96028
9-3-2/M82	1.42915	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00334	1
IL2-6/WTpooled	0.92908	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.82853	0.294
IL12-4/WTpooled	0.93731	0.71
IL1-4/WTpooled	1.01956	1
WT/WTpooled	0.93789	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	0.94739	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93882	0.807
DC3000/delta hrp 6h	0.93753	0.95
DC3000/delta hrp 12h	0.95059	1
DC3000/delta hrp 24h	0.77216	0.072

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51301	0.037
DC3000 delta B/DC3000 delta AB	0.68894	0.125

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.79406	1
Exp 36h	0.70126	0.589
Exp 60h	0.8312	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02017	1
Var 0h	1.07316	0.782
Var 12h I row2-row1	0.81207	0.318
Var 12h NI row2-row1	1.05063	1
Var 36h I row2-row1	1.10648	1
Var 36h NI row2-row1	0.92195	0.482
Var 60h I row2-row1	2.03778	0.562
Var 60h NI row2-row1	0.93988	1
Time course 0hI-0hNI	0.92378	0.461
Time course 12hI-12hNI	0.98925	0.968
Time course 36hI-36hNI	0.85222	0.121
Time course 60hI-60hNI	0.15869	0.005

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)	1.11779	0.408
transgenic ySAMdc/azygous control (breaker)	2.37053	0.162
transgenic ySAMdc/azygous control (red)	1.37624	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99297	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.62086	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.10858	0.083
Manapal/WT (break)	1.63126	0.381
Manapal/WT (red)	2.08255	0.126