Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.7.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.04677	0.615
27DAP/17DAP	1.4583	0.671
39DAP/27DAP	1.33649	0.638
41DAP/39DAP	0.75523	0.285
42DAP/41DAP	1.62977	0.256
43DAP/42DAP	0.97198	0.918
47DAP/43DAP	0.85013	0.625
52DAP/47DAP	1.13025	0.915
57DAP/52DAP	0.95172	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97168	0.526
17DAP/reference	0.81393	0.031
27DAP/reference	0.97716	0.623
39DAP/reference	0.82781	0.074
41DAP/reference	0.69601	0.009
42DAP/reference	1.00776	0.665
43DAP/reference	1.00854	0.982
47DAP/reference	1.02887	0.728
52DAP/reference	0.97576	0.53
57DAP/reference	1.16202	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98678	0.763
27DAP/17DAP	1.01738	0.957
39DAP/27DAP	1.60595	0.054
41DAP/39DAP	1.11542	0.801
42DAP/41DAP	0.93241	0.538
43DAP/42DAP	1.79787	0.015
47DAP/43DAP	1.07709	0.756
52DAP/47DAP	1.23694	0.489
57DAP/52DAP	1.75557	0.029
57DAP/7DAP	2.09486	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.83445	0.027
17DAP/reference	1.80299	0.011
27DAP/reference	1.04117	0.301
39DAP/reference	0.89197	0.17
41DAP/reference	0.87767	0.06
42DAP/reference	1.12212	0.889
43DAP/reference	1.13543	0.2
47DAP/reference	0.82273	0.128
52DAP/reference	0.742	0.017
57DAP/reference	1.09007	0.288

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98627	0.756
17DAP/reference	1.02864	0.92
27DAP/reference	1.20496	0.114
39DAP/reference	1.05202	0.725
41DAP/reference	1.16958	0.094
42DAP/reference	0.99893	0.655
43DAP/reference	0.88078	0.263
47DAP/reference	0.91801	0.154
52DAP/reference	0.92929	0.327
57DAP/reference	0.8794	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.59371	0.016
17DAP/reference	1.73034	0.45
27DAP/reference	2.08194	0.017
39DAP/reference	1.31477	0.151
41DAP/reference	1.02978	0.984
42DAP/reference	0.94913	0.552
43DAP/reference	0.97481	0.545
47DAP/reference	1.17737	0.029
52DAP/reference	0.86036	0.296
57DAP/reference	1.18046	0.444

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90248	1
26DAP/20DAP	0.96846	1
34DAP/26DAP	0.95169	0.893
51DAP/34DAP	0.89693	0.513
52DAP/51DAP	0.93229	1
53DAP/52DAP	0.59375	0.078
55DAP/53DAP	0.65477	0.077
57DAP/55DAP	1.54945	0.265
62DAP/57DAP	1.58188	0.047
68DAP/62DAP	1.39265	0.845
68DAP/14DAP	1.12274	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.72481	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.674	0.178
Mature Green Tomato/Ripe Tomato	0.68803
Immature Eggplant/Mature Eggplant	0.60624	0.062
Ripe Pepper/Ripe Tomato	0.50123	0.224
Mature Eggplant/Ripe Tomato	0.43054	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06893	1
1-1-2/M82	1.14634	1
12-2/M82	1.06008	1
12-4/M82	1.01478	1
1-3/M82	1.37667	0.479
2-1-1/M82	1.0347	1
2-1/M82	0.87689	0.322
2-6/M82	0.85207	0.501
3-2/M82	1.59057
4-1-1/M82	1.04286	1
4-1/M82	1.0943
4-3-2/M82	0.68431	0.487
4-3/M82	0.8208	0.578
5-3/M82	0.91623	1
6-2/M82	1.71899	1
6-3/M82	0.92626	0.715
7-1/M82	1.1496	1
7-2/M82	0.98684	1
9-3-2/M82	0.96774	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04607	1
IL2-6/WTpooled	0.98076	1
IL7-5/WTpooled	0.76388	1
IL7-3/WTpooled	1.11047	1
IL12-4/WTpooled	0.92682	1
IL1-4/WTpooled	0.83421	0.415
WT/WTpooled	1.08067	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	1.30542	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12616	0.894
DC3000/delta hrp 6h	0.92508	0.95
DC3000/delta hrp 12h	1.03168	1
DC3000/delta hrp 24h	1.24661	0.174

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.49335	0.042
DC3000 delta B/DC3000 delta AB	1.47423	0.115

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.28777	1
Exp 36h	1.04291	1
Exp 60h	1.07757	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96084	1
Var 0h	0.96662	1
Var 12h I row2-row1	0.94334	0.565
Var 12h NI row2-row1	1.04731	1
Var 36h I row2-row1	1.17899	0.339
Var 36h NI row2-row1	0.95092	0.645
Var 60h I row2-row1	0.79418	0.439
Var 60h NI row2-row1	0.85049	0.516
Time course 0hI-0hNI	1.07049	0.377
Time course 12hI-12hNI	0.98764	0.95
Time course 36hI-36hNI	1.52549	0.007
Time course 60hI-60hNI	2.06916	0.008

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)	1.02187	0.921
transgenic ySAMdc/azygous control (breaker)	0.79285	0.173
transgenic ySAMdc/azygous control (red)	1.12419	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.37175	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74068	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05055	0.14
Manapal/WT (break)	0.99893	1
Manapal/WT (red)	0.95157	0.607