Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.11.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87323	0.303
27DAP/17DAP	0.75024	0.354
39DAP/27DAP	0.90921	0.62
41DAP/39DAP	0.84732	0.409
42DAP/41DAP	0.78042	0.774
43DAP/42DAP	1.01814	0.931
47DAP/43DAP	0.87263	0.546
52DAP/47DAP	0.74758	0.471
57DAP/52DAP	0.87032	0.899

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26512	0.008
17DAP/reference	1.25765	0.037
27DAP/reference	1.05092	0.771
39DAP/reference	0.95282	0.68
41DAP/reference	1.45169	0.016
42DAP/reference	1.1854	0.431
43DAP/reference	0.97989
47DAP/reference	0.81876	0.046
52DAP/reference	0.78401	0.012
57DAP/reference	0.84808	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68187	0.048
27DAP/17DAP	1.53163	0.027
39DAP/27DAP	0.54685	0.044
41DAP/39DAP	1.55222	0.073
42DAP/41DAP	0.83678	0.106
43DAP/42DAP	0.64655	0.022
47DAP/43DAP	0.96999	0.846
52DAP/47DAP	1.04708	0.979
57DAP/52DAP	0.96491	0.782
57DAP/7DAP	0.65659	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86579	0.03
17DAP/reference	1.44625	0.008
27DAP/reference	1.6036	0.007
39DAP/reference	0.95708	0.307
41DAP/reference	1.09025	0.402
42DAP/reference	0.95653	0.151
43DAP/reference	1.03489	0.672
47DAP/reference	0.92192	0.504
52DAP/reference	0.82864	0.053
57DAP/reference	0.97816	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40547	0.054
17DAP/reference	1.6874	0.01
27DAP/reference	1.30697	0.029
39DAP/reference	1.02422	1
41DAP/reference	0.92684	0.299
42DAP/reference	1.02402	0.987
43DAP/reference	1.07712	0.362
47DAP/reference	0.9638	0.359
52DAP/reference	1.09925	0.559
57DAP/reference	1.47709	0.221

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6327	0.015
17DAP/reference	1.37664	0.153
27DAP/reference	1.33103	0.021
39DAP/reference	1.22656	0.012
41DAP/reference	1.14799	0.029
42DAP/reference	0.93755	0.445
43DAP/reference	0.90515	0.365
47DAP/reference	0.86151	0.224
52DAP/reference	0.87118	0.342
57DAP/reference	0.61956	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1499	0.966
26DAP/20DAP	1.38364	0.133
34DAP/26DAP	0.95395	0.898
51DAP/34DAP	1.03919	0.962
52DAP/51DAP	1.1378	0.616
53DAP/52DAP	1.33767	0.125
55DAP/53DAP	0.97381	0.784
57DAP/55DAP	1.41294	0.311
62DAP/57DAP	0.55923	0.005
68DAP/62DAP	1.33652	0.759
68DAP/14DAP	1.77259

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56193	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.01741	0.058
Mature Green Tomato/Ripe Tomato	8.91778	0.015
Immature Eggplant/Mature Eggplant	1.1175	0.288
Ripe Pepper/Ripe Tomato	13.1206
Mature Eggplant/Ripe Tomato	19.1432	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.21252	0.655
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	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	N/A	N/A
5-3/M82	1.66205
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.75749
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08461	0.493
IL2-6/WTpooled	0.97991	1
IL7-5/WTpooled	0.75901	1
IL7-3/WTpooled	0.96623	1
IL12-4/WTpooled	1.08453	0.785
IL1-4/WTpooled	0.89048	0.476
WT/WTpooled	0.98186	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	1.00064	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0832	0.921
DC3000/delta hrp 6h	0.84509	0.942
DC3000/delta hrp 12h	0.94413	1
DC3000/delta hrp 24h	1.06823	1

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	0.89978	0.529

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90477	1
Exp 36h	0.87583	0.82
Exp 60h	0.87672	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00053	1
Var 0h	0.92894	0.933
Var 12h I row2-row1	1.0772	0.795
Var 12h NI row2-row1	1.23127	0.34
Var 36h I row2-row1	1.02978	1
Var 36h NI row2-row1	0.5879	0.432
Var 60h I row2-row1	1.40085	1
Var 60h NI row2-row1	0.83607	0.458
Time course 0hI-0hNI	0.94486	0.639
Time course 12hI-12hNI	1.01414	0.82
Time course 36hI-36hNI	0.97593	0.549
Time course 60hI-60hNI	0.55866	0.006

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)	0.99237	0.931
transgenic ySAMdc/azygous control (breaker)	2.38718	0.248
transgenic ySAMdc/azygous control (red)	1.13028	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.74972	0.343

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55464	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86722	0.172
Manapal/WT (break)	0.50995	0.333
Manapal/WT (red)	1.30532	0.413