MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Gene	description	Value Type	Rank	Filtered	Network Comparison Type	Interaction Map	green	network_comparison	red

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Showing element 3180 to 3229 of 3730 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Rank	Filtered	green	network_comparison	red
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	2619	1	219.722	1.00137	220.024
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]	2512		234.948	1.00241	234.384
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]	2513
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	941		205.083	1.03586	212.437
symplekin. [swissprot;acc:q92797]	2203		163.8	1.00651	162.741
synapsin i (brain protein 4.1). [swissprot;acc:p17600]	669		216.576	1.0577	229.072
synapsin ii. [swissprot;acc:q92777]	662
synapsin iii. [swissprot;acc:o14994]	657
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	814		221.785	1.04425	212.386
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01]	2351		213.289	1.00438	214.223
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	56	0	16388	1.36929	22440
	566	1	121.261	1.06563	129.219
syndecan-3 (synd3). [swissprot;acc:o75056]	2862		0.00001	1	0.00001
syntaxin 10 (syn10). [swissprot;acc:o60499]	54	0	19014.6	1.36949	13884.4
	354	1	257.442	1.09694	234.691
syntaxin 12. [refseq;acc:nm_177424]	858		208.997	1.04043	217.446
syntaxin 16 (syn16). [swissprot;acc:o14662]	809		221.785	1.04425	212.386
syntaxin 18. [swissprot;acc:q9p2w9]	237		254.15	1.11785	227.357
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	84	0	15781	1.26647	12460.6
	811	1	221.785	1.04425	212.386
syntaxin 1b. [swissprot;acc:q15531]	815
syntaxin 5. [swissprot;acc:q13190]	2866		0.00001	1	0.00001
syntaxin 6. [swissprot;acc:o43752]	355		257.414	1.09691	234.673
syntaxin 7. [swissprot;acc:o15400]	890		209.012	1.03908	217.181
t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]	2771		0.00001	1	0.00001
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	2042		208.803	1.00854	210.586
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	434		229.411	1.07934	212.547
t-cell activation wd repeat protein. [refseq;acc:nm_139281]	976		235.322	1.03407	243.34
t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542]	2865		0.00001	1	0.00001
t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]	2760
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]	585		252.492	1.06411	237.28
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]	584
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	581
t-complex 11. [refseq;acc:nm_018679]	1741		209.258	1.01289	206.595
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	1044		178.889	1.03121	173.475
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	689		128.225	1.05579	135.379
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	285		203.242	1.10532	224.647
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643]	1040		168.359	1.03136	163.24
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	397		101.613	1.08932	110.689
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	192	0	11333.2	1.122	12715.9
	2917	1	0.00001	1	0.00001
t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [swissprot;acc:q92526]	2995
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	112		267.246	1.24557	332.874
t54 protein. [swissprot;acc:q92917]	569		212.38	1.06554	226.3
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	180		298.438	1.16474	256.228
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	1017		210.558	1.03233	217.365
target of myb protein 1. [swissprot;acc:o60784]	948		209.824	1.03541	217.254
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	952		209.83	1.03537	217.252
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]	2267		210.416	1.00561	211.597
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	382		183.66	1.09328	200.791

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.