Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.4.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04424	0.878
27DAP/17DAP	1.16562	0.836
39DAP/27DAP	0.71558	0.301
41DAP/39DAP	1.95515	0.339
42DAP/41DAP	1.06677	0.978
43DAP/42DAP	0.94483	0.829
47DAP/43DAP	1.54226	0.23
52DAP/47DAP	1.09146	0.949
57DAP/52DAP	1.06856	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92313	0.238
17DAP/reference	0.89637	0.24
27DAP/reference	1.00104	0.904
39DAP/reference	0.98824	0.828
41DAP/reference	0.89939	0.039
42DAP/reference	0.97511	0.305
43DAP/reference	1.15944	0.061
47DAP/reference	1.16409	0.001
52DAP/reference	1.13094	0.04
57DAP/reference	1.15794	0.057

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05338	0.858
27DAP/17DAP	1.10566	0.617
39DAP/27DAP	1.04856	0.832
41DAP/39DAP	1.01216	1
42DAP/41DAP	1.07499	0.663
43DAP/42DAP	0.956	0.618
47DAP/43DAP	1.06345	0.699
52DAP/47DAP	1.1107	0.718
57DAP/52DAP	1.06068	0.813
57DAP/7DAP	1.60102	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90705	0.1
17DAP/reference	0.88081	0.064
27DAP/reference	0.88458	0.117
39DAP/reference	1.04812	0.819
41DAP/reference	1.00765	1
42DAP/reference	0.91891	0.222
43DAP/reference	0.79561	0.018
47DAP/reference	1.04321	0.776
52DAP/reference	0.74982	0.012
57DAP/reference	0.94116	0.291

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95457	0.532
17DAP/reference	0.82211	0.015
27DAP/reference	0.98339	0.576
39DAP/reference	0.85891	0.214
41DAP/reference	0.86215	0.268
42DAP/reference	0.99338	0.655
43DAP/reference	1.02741	0.957
47DAP/reference	0.91924	0.066
52DAP/reference	0.96524	0.469
57DAP/reference	0.86177	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88714	0.127
17DAP/reference	0.9124	0.275
27DAP/reference	0.83083	0.044
39DAP/reference	0.79664	0.025
41DAP/reference	0.83816	0.019
42DAP/reference	0.82628	0.108
43DAP/reference	0.89193	0.226
47DAP/reference	1.17062	0.127
52DAP/reference	0.8683	0.262
57DAP/reference	1.5233	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21356	0.966
26DAP/20DAP	1.05902	0.826
34DAP/26DAP	1.16019	1
51DAP/34DAP	0.95687	0.722
52DAP/51DAP	1.01672	0.888
53DAP/52DAP	1.08283	0.594
55DAP/53DAP	1.21942	0.21
57DAP/55DAP	0.98317	0.909
62DAP/57DAP	0.91709	0.871
68DAP/62DAP	0.78499	0.641
68DAP/14DAP	1.08613	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15625	0.105

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.73177	0.221
Mature Green Tomato/Ripe Tomato	0.73761	0.029
Immature Eggplant/Mature Eggplant	0.78232	0.197
Ripe Pepper/Ripe Tomato	0.84535	0.293
Mature Eggplant/Ripe Tomato	0.72484	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02981	1
1-1-2/M82	0.97586	1
12-2/M82	1.17976	1
12-4/M82	0.81966	0.619
1-3/M82	0.99174	0.501
2-1-1/M82	1.09851
2-1/M82	0.79478	0.74
2-6/M82	1.14995	0.695
3-2/M82	1.10356
4-1-1/M82	0.9277	1
4-1/M82	0.94729	1
4-3-2/M82	0.80699	0.698
4-3/M82	0.82841	0.72
5-3/M82	1.03687	1
6-2/M82	0.85679	0.497
6-3/M82	1.01375
7-1/M82	N/A	N/A
7-2/M82	0.953	0.881
9-3-2/M82	0.89398	0.355

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	0.73867
IL12-4/WTpooled	0.89586	0.71
IL1-4/WTpooled	1.27596
WT/WTpooled	1.22739	0.686

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	1.04369	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07662	0.758
DC3000/delta hrp 6h	1.01145	0.95
DC3000/delta hrp 12h	0.98001	1
DC3000/delta hrp 24h	1.03441	0.673

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	0.74956	0.347

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01086	1
Exp 36h	0.88864	0.449
Exp 60h	0.89121	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.08907	0.421
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.97029	0.454
transgenic ySAMdc/azygous control (breaker)	0.8994	0.49
transgenic ySAMdc/azygous control (red)	0.932	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02882	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1404	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94682	1
Manapal/WT (break)	1.06358	1
Manapal/WT (red)	1.33263	0.126