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

Results: HTML CSV LaTeX

Showing element 1913 to 1962 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

red	Rank	description	green	network_comparison
5816.12	1809	epsin 3. [refseq;acc:nm_017957]	6196.21	1.06535
5817.07	2090	kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685]	6138.59	1.05527
5817.41	2092	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	6138.8	1.05525
5817.56	2093	fuse binding protein 3 (fragment). [sptrembl;acc:q92946]	6138.9	1.05524
5819.36	2247	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	6092.93	1.04701
5819.37	1569	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	6239.55	1.0722
5819.39	1546	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	6244.37	1.07303
5822.25	1567	26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	6242.94	1.07226
5825.61	2170	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	6126.74	1.05169
	2171	phd finger protein 9. [refseq;acc:nm_018062]
	2172	small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
5826	1883	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	6195.48	1.06342
	1884	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
	1885	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]
	1886	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
5826.29	1171	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	6335.93	1.08747
5826.32	1172	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	6335.95
5826.34	1170	ubiquitin-like protein smt3a. [swissprot;acc:p55854]	6335.98
5826.74	1609	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	6242.44	1.07134
5829.51	1773	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	6218.11	1.06666
5829.61	1764	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884]	6218.27	1.06667
	1765	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]
	1766	nitrilase 1. [refseq;acc:nm_005600]
	1767	utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]
	1768	lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182]
	1769	dystrophin. [swissprot;acc:p11532]
	1770	angiomotin. [refseq;acc:nm_133265]
	1771	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
	1772	alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424]
5829.73	1763	dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	6218.45	1.06668
5829.74	1987	peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331]	6175.69	1.05934
5830.03	1984	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	6176.1	1.05936
5830.46	1980	bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701]	6176.71	1.05939
5832.13	1162	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	6343.59	1.0877
	1163	elks protein. [refseq;acc:nm_015064]
5833.01	2248	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	6106.48	1.04688
5835.15	2088	presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959]	6159.11	1.05552
5835.4	2085	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	6159.4
5835.44	2086	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352]	6159.45
5835.45	2087	presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]	6159.46
5837.34	2080	r3h domain protein 1. [swissprot;acc:q15032]	6162.91	1.05577
5838.01	2184	rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9]	6132.35	1.05042
5838.87	1150	mstp028 protein. [refseq;acc:nm_031954]	6355.06	1.08841
5839.72	1789	serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4]	6227.33	1.06637
	1790	kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241]
	1791	serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9]
	1792	serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965]
	1793	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
5840.01	1153	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	6355.56	1.08828
5840.54	2252	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161]	6113.01	1.04665

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.