Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.10.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86981	0.389
27DAP/17DAP	1.19543	0.833
39DAP/27DAP	1.03261	0.84
41DAP/39DAP	1.14757	0.624
42DAP/41DAP	0.94862	1
43DAP/42DAP	1.05116	1
47DAP/43DAP	1.37668	0.633
52DAP/47DAP	0.95178	0.823
57DAP/52DAP	0.89644	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11414	0.241
17DAP/reference	1.0238	0.764
27DAP/reference	0.98264	0.694
39DAP/reference	0.99712	0.921
41DAP/reference	0.96395	0.667
42DAP/reference	0.96232	0.196
43DAP/reference	0.96107	0.594
47DAP/reference	1.0362	0.885
52DAP/reference	0.93202	0.244
57DAP/reference	1.02801	0.783

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95912	0.526
27DAP/17DAP	1.01051	0.973
39DAP/27DAP	1.01717	0.779
41DAP/39DAP	1.34402	0.007
42DAP/41DAP	0.95644	0.644
43DAP/42DAP	0.85374	0.082
47DAP/43DAP	1.0644	0.681
52DAP/47DAP	1.07526	0.776
57DAP/52DAP	0.9177	0.436
57DAP/7DAP	1.08049	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92861	0.402
17DAP/reference	0.84266	0.028
27DAP/reference	0.9113	0.076
39DAP/reference	1.00883	1
41DAP/reference	1.00055	0.646
42DAP/reference	0.91336	0.262
43DAP/reference	0.85931	0.241
47DAP/reference	0.86921	0.168
52DAP/reference	0.73339	0.009
57DAP/reference	0.82119	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35355	0.1
17DAP/reference	1.24463	0.063
27DAP/reference	1.14185	0.149
39DAP/reference	0.97067	0.485
41DAP/reference	0.93069	0.173
42DAP/reference	1.09123	0.445
43DAP/reference	1.51395	0.024
47DAP/reference	0.98199	0.527
52DAP/reference	1.11716	0.528
57DAP/reference	0.97549	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97042	0.526
17DAP/reference	1.17184	0.084
27DAP/reference	0.86789	0.052
39DAP/reference	0.99634	0.693
41DAP/reference	0.93439	0.459
42DAP/reference	1.0165	0.818
43DAP/reference	1.03997	0.667
47DAP/reference	1.13383	0.324
52DAP/reference	3.93214	0.592
57DAP/reference	0.97403	0.602

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00941	1
26DAP/20DAP	1.00885	1
34DAP/26DAP	1.15148	0.304
51DAP/34DAP	1.50369	0.047
52DAP/51DAP	1.07999	0.238
53DAP/52DAP	1.00642	0.998
55DAP/53DAP	0.86731	0.336
57DAP/55DAP	1.00506	0.938
62DAP/57DAP	1.31156	0.935
68DAP/62DAP	1.07975	0.914
68DAP/14DAP	0.94316	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.60758	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.51876	0.115
Mature Green Tomato/Ripe Tomato	0.98489	0.774
Immature Eggplant/Mature Eggplant	1.06108	0.348
Ripe Pepper/Ripe Tomato	2.2545	0.256
Mature Eggplant/Ripe Tomato	2.06218	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09684	0.877
1-1-2/M82	0.99649	1
12-2/M82	1.2168	1
12-4/M82	0.96565	1
1-3/M82	0.7829	0.378
2-1-1/M82	1.0563	0.689
2-1/M82	0.85504	0.325
2-6/M82	0.92131	0.501
3-2/M82	0.90011	0.455
4-1-1/M82	0.94116	1
4-1/M82	1.05601	1
4-3-2/M82	0.99122	1
4-3/M82	1.14145	1
5-3/M82	0.99504	1
6-2/M82	0.63181
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.09685
9-3-2/M82	0.8913	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09665	1
IL2-6/WTpooled	0.96834	1
IL7-5/WTpooled	0.94631	1
IL7-3/WTpooled	1.05905	1
IL12-4/WTpooled	0.51418	0.554
IL1-4/WTpooled	0.91797	0.834
WT/WTpooled	0.91994	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	0.98877	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02168	0.921
DC3000/delta hrp 6h	1.01147	1
DC3000/delta hrp 12h	1.22478	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23436	0.648
DC3000 delta B/DC3000 delta AB	1.00456	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81839	1
Exp 36h	0.70495	0.426
Exp 60h	0.75395	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99491	1
Var 0h	0.83532	0.933
Var 12h I row2-row1	0.8295	0.338
Var 12h NI row2-row1	0.96301	0.906
Var 36h I row2-row1	1.11087	0.908
Var 36h NI row2-row1	1.12972	1
Var 60h I row2-row1	0.84247	0.287
Var 60h NI row2-row1	1.01432	1
Time course 0hI-0hNI	0.93379	0.617
Time course 12hI-12hNI	1.01153	0.888
Time course 36hI-36hNI	1.07464	0.28
Time course 60hI-60hNI	0.72426	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)	1.25581	0.25
transgenic ySAMdc/azygous control (breaker)	0.94366	0.49
transgenic ySAMdc/azygous control (red)	1.09824	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01326	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.49257	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.62299	0.093
Manapal/WT (break)	2.26388	0.14
Manapal/WT (red)	1.46587	0.164