Example 1


Take a set of promoters of upregulated genes upon TNF-alpha stimulation and use it as the POSITIVE sequence set in CMA. Use the downregulated genes as NEGATIVE sequence set.

You can take the sets here:
<1100bp promoters of upregulated genes>
<1100bp promoters of downregulated genes>


Example 2


Take a set of promoters of T-cell specific genes and use it as the POSITIVE sequence set in CMA.

You can take the set here:
<1100bp promoters of T-cell specific genes>

Take a set of promoters of 100 housekeeping genes as the NEGATIVE sequence set. (please use the option "Load default NEGATIVE sequences")


Please, specify the search parameters according to the screenshot above.
Press "Run" and after a while you will be able to get the following results:

Promoter model
<–V$GATA3_02–> [6…21] <–V$NFAT_Q6—
<–V$SP1_Q6–> [12…12] <–V$NFKB_C—
<–V$LYF1_01–> [9…30] <–V$IRF1_01–>
<–V$EGR3_01–> [10…11] <–V$AML1_01–>
<–V$TAL1ALPHAE47_01— [19…25] <–V$CEBPB_02–>
<–V$AP1_Q4–> [4…8] <–V$OCT1_07–> 
                        Goal function calculation
--------------------------------------------------------------------------
      Elements         R         T         E         N         P     Total  
--------------------------------------------------------------------------
         Value  0.421110  0.846934  0.870000  0.980000  1.000000            
        Weight  0.200000  0.200000  0.200000  0.200000  0.200000  1.000000  
Weighted value  0.084222  0.169387  0.174000  0.196000  0.200000  0.823609


Expression-score distribution


Yes-No distribution

Matrix names and corresponding colors



Sites on sequences
Arrows Seqence id Sequence score Sequence type
HSA_1437_CSF2 0.235622 Pos
HSA_1960_EGR3 0.167090 Pos
HSA_3383_ICAM1 0.192587 Pos
HSA_3458_IFNG 0.117683 Pos
HSA_3558_IL2 0.196938 Pos
HSA_3562_IL3 0.172157 Pos
HSA_3565_IL4 0.190516 Pos
HSA_356_FASLG 0.200028 Pos
HSA_5468_PPARG 0.192077 Pos
HSA_5743_PTGS2 0.233485 Pos
HSA_7124_TNF 0.244484 Pos
MMU_12902_Cr2 0.197417 Pos
MMU_12981_Csf2 0.217797 Pos
MMU_14103_Fasl 0.250866 Pos
MMU_16160_Il12b 0.211396 Pos
MMU_16183_Il2 0.194449 Pos
MMU_16189_Il4 0.206945 Pos
MMU_16191_Il5 0.224943 Pos
RNO_24505_Ins1 0.182379 Pos
RNO_24952_Gcg 0.192266 Pos
NM_006389 0.151658 Neg
NM_006411 0.169165 Neg
NM_006429 0.158948 Neg
NM_006460 0.148565 Neg
NM_006510 0.142882 Neg
NM_006513 0.204081 Neg
NM_006570 0.126518 Neg
NM_006597 0.069584 Neg
NM_006623 0.159793 Neg
NM_006666 0.049176 Neg
NM_006688 0.105495 Neg
NM_006694 0.134355 Neg
NM_006711 0.171141 Neg
NM_006743 0.126514 Neg
NM_006782 0.112569 Neg
NM_006867 0.153530 Neg
NM_006888 0.199158 Neg
NM_006899 0.197286 Neg
NM_006937 0.055570 Neg
NM_007067 0.224209 Neg
NM_007103 0.143998 Neg
NM_007104 0.111736 Neg
NM_007144 0.101163 Neg
NM_007182 0.057361 Neg
NM_007209 0.053518 Neg
NM_007245 0.000000 Neg
NM_007260 0.139839 Neg
NM_007262 0.162981 Neg
NM_007263 0.181592 Neg
NM_007278 0.121041 Neg
NM_007285 0.053481 Neg
NM_007286 0.115941 Neg
NM_007355 0.135427 Neg
NM_007359 0.091551 Neg
NM_007363 0.152489 Neg
NM_007369 0.074522 Neg
NM_012099 0.129994 Neg
NM_012127 0.047934 Neg
NM_012138 0.211970 Neg
NM_012179 0.125909 Neg
NM_012407 0.094395 Neg
NM_013232 0.171156 Neg
NM_013234 0.107047 Neg
NM_013310 0.160948 Neg
NM_014225 0.051331 Neg
NM_014228 0.180580 Neg
NM_014231 0.244569 Neg
NM_014281 0.065492 Neg
NM_014390 0.000000 Neg
NM_014402 0.088523 Neg
NM_014453 0.051697 Neg
NM_014508 0.159141 Neg
NM_014604 0.106879 Neg
NM_014610 0.160515 Neg
NM_014754 0.104765 Neg
NM_014764 0.184077 Neg
NM_014916 0.138915 Neg
NM_014972 0.055220 Neg
NM_015024 0.263441 Neg
NM_015292 0.217956 Neg
NM_015343 0.045622 Neg
NM_015680 0.124681 Neg
NM_016292 0.118307 Neg
NM_017432 0.054680 Neg
NM_017797 0.092149 Neg
NM_017828 0.141743 Neg
NM_018955 0.288373 Neg
NM_018975 0.128624 Neg
NM_019059 0.161884 Neg
NM_019884 0.136109 Neg
NM_020151 0.181621 Neg
NM_020195 0.195244 Neg
NM_020529 0.137734 Neg
NM_021019 0.163151 Neg
NM_021074 0.069260 Neg
NM_021103 0.139736 Neg
NM_021107 0.056388 Neg
NM_021128 0.051130 Neg
NM_021642 0.149356 Neg
NM_021959 0.078196 Neg
NM_021960 0.132158 Neg
NM_021974 0.124200 Neg
NM_021975 0.057103 Neg
NM_021983 0.170533 Neg
NM_022830 0.150058 Neg
NM_023009 0.053142 Neg
NM_024011 0.101289 Neg
NM_024069 0.180974 Neg
NM_024798 0.116355 Neg
NM_030662 0.104685 Neg
NM_030796 0.000000 Neg
NM_031420 0.125621 Neg
NM_032348 0.116477 Neg
NM_032378 0.109118 Neg
NM_032635 0.129544 Neg
NM_032801 0.166617 Neg
NM_033142 0.110264 Neg
NM_033546 0.182087 Neg
NM_133476 0.220130 Neg
NM_144565 0.132154 Neg