Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.19.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84989	0.445
27DAP/17DAP	1.02877	1
39DAP/27DAP	1.60348	0.426
41DAP/39DAP	0.5648	N/A
42DAP/41DAP	0.83195	1
43DAP/42DAP	0.9669	0.909
47DAP/43DAP	1.10287	1
52DAP/47DAP	1.52558	0.731
57DAP/52DAP	1.08142	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00135	0.844
17DAP/reference	0.98047	0.63
27DAP/reference	1.01592	0.925
39DAP/reference	1.11649	0.359
41DAP/reference	1.09624	0.034
42DAP/reference	0.89675	0.015
43DAP/reference	0.97737	0.728
47DAP/reference	0.94602	0.148
52DAP/reference	0.94056	0.319
57DAP/reference	0.99055	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22298	0.455
27DAP/17DAP	1.04487	0.942
39DAP/27DAP	1.00439	1
41DAP/39DAP	1.06598	0.909
42DAP/41DAP	0.97913	0.759
43DAP/42DAP	0.91887	0.399
47DAP/43DAP	0.87644	0.332
52DAP/47DAP	1.15914	0.573
57DAP/52DAP	1.30923	0.703
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43322	0.061
17DAP/reference	1.92589	0.006
27DAP/reference	1.63715	0.006
39DAP/reference	2.10233	0.005
41DAP/reference	2.0054	0.009
42DAP/reference	2.34774	0.006
43DAP/reference	2.53847	0.007
47DAP/reference	1.51491	0.279
52DAP/reference	1.98781	0.008
57DAP/reference	1.69995	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97256	0.669
17DAP/reference	0.94179	0.337
27DAP/reference	0.88937	0.188
39DAP/reference	0.91854	0.117
41DAP/reference	0.85234	0.054
42DAP/reference	0.9513	0.289
43DAP/reference	0.92303	0.414
47DAP/reference	0.96649	0.379
52DAP/reference	0.9987	0.666
57DAP/reference	1.14651	0.033

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45974	0.103
17DAP/reference	1.16492	0.657
27DAP/reference	1.90452	0.027
39DAP/reference	1.72751	0.015
41DAP/reference	1.66038	0.007
42DAP/reference	1.76659	0.019
43DAP/reference	1.57082	0.1
47DAP/reference	0.8905	0.215
52DAP/reference	1.88622	0.079
57DAP/reference	1.34313	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25491	0.966
26DAP/20DAP	1.14177	0.931
34DAP/26DAP	0.82156	0.712
51DAP/34DAP	0.85662	0.598
52DAP/51DAP	0.86667	1
53DAP/52DAP	1.51405	0.134
55DAP/53DAP	0.66094	N/A
57DAP/55DAP	1.16275	0.881
62DAP/57DAP	1.33913	0.257
68DAP/62DAP	1.02222	1
68DAP/14DAP	1.15746	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.35077	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04534	1
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.71617	N/A
Ripe Pepper/Ripe Tomato	0.58447	0.224
Mature Eggplant/Ripe Tomato	0.7128	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85887	N/A
1-1-2/M82	0.8208	1
12-2/M82	N/A	N/A
12-4/M82	0.90566	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.87945	1
2-1/M82	0.69766	N/A
2-6/M82	0.79478	N/A
3-2/M82	0.8906	N/A
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	0.88735	1
5-3/M82	1.15885	1
6-2/M82	N/A	N/A
6-3/M82	1.16029	1
7-1/M82	0.98552	N/A
7-2/M82	0.99676	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87084	0.321
IL2-6/WTpooled	1.25157	0.46
IL7-5/WTpooled	2.04939	0.792
IL7-3/WTpooled	0.71449	0.294
IL12-4/WTpooled	1.03307	0.839
IL1-4/WTpooled	1.39295	0.426
WT/WTpooled	1.01478	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	1.1919	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05019	1
DC3000/delta hrp 6h	0.90587	0.95
DC3000/delta hrp 12h	0.99565	1
DC3000/delta hrp 24h	1.78706	0.079

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8412	1
Exp 36h	1.40996	1
Exp 60h	1.02826	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96459	1
Var 0h	0.70283	0.457
Var 12h I row2-row1	1.03389	0.473
Var 12h NI row2-row1	0.98802	1
Var 36h I row2-row1	1.08368	1
Var 36h NI row2-row1	1.1015	1
Var 60h I row2-row1	0.76734	0.832
Var 60h NI row2-row1	1.00075	1
Time course 0hI-0hNI	1.12204	0.867
Time course 12hI-12hNI	1.04699	0.81
Time course 36hI-36hNI	1.24466	0.044
Time course 60hI-60hNI	1.41139	0.16

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)	1.11543	0.312
transgenic ySAMdc/azygous control (breaker)	0.83419	0.251
transgenic ySAMdc/azygous control (red)	0.96175	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05167	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24106	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88377	1
Manapal/WT (break)	1.00136	1
Manapal/WT (red)	1.32154	0.222