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

Results: HTML CSV LaTeX

Showing element 1551 to 1600 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
776	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	Subtracted	5317.78	5944.25	626.47
	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]	Divided	5874.76	6533.36	1.11211
777	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]		5874.74	6533.34
	z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]	Subtracted	5317.78	5944.25	626.47
778	pp1201 protein. [refseq;acc:nm_022152]
	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313]	Divided	5874.63	6533.23	1.11211
779	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]		5874.76	6533.36
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Subtracted	5317.78	5944.25	626.47
780	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]
	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8]	Divided	5874.76	6533.36	1.11211
781	secretory pathway component sec31b-1. [refseq;acc:nm_015490]
	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]	Subtracted	5317.78	5944.25	626.47
782	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]		6324.31	6948.5	624.19
	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]	Divided	5874.74	6533.33	1.11211
783	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	Subtracted	6289.72	6911.96	622.24
	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]	Divided	5874.78	6533.37	1.1121
784	cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]	Subtracted	6289.72	6911.96	622.24
	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543]	Divided	5874.77	6533.36	1.1121
785	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]		4997	5557.17
	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]	Subtracted	6289.72	6911.96	622.24
786	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815]		6499.89	7121.77	621.88
	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	Divided	9304.83	10347.3	1.11204
787	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621]	Subtracted	9720.64	9099.1	621.54
	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]	Divided	5890.49	6547.9	1.11161
788	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	Subtracted	6472.38	7092.65	620.27
	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488]	Divided	5890.41	6547.81	1.11161
789	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]		5890.59	6547.99	1.1116
	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	Subtracted	6167.33	6785.98	618.65
790	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]		6165.1	6783.01	617.91
	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050]	Divided	5890.88	6548.28	1.1116
791	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	Subtracted	6544.26	7159.43	615.17
	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	Divided	4025.3	4474.3	1.11154
792	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]		6772.75	7526.2	1.11125
	target of myb protein 1. [swissprot;acc:o60784]	Subtracted	5640.79	6255.85	615.06
793	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]		5641.11	6255.99	614.88
	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	Divided	5036.92	5596.36	1.11107
794	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]		6441.17	7154.55	1.11075
	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	Subtracted	5641.12	6255.99	614.87
795	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Divided	6441.14	7154.13	1.11069
	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	Subtracted	5641.53	6256.17	614.64
796	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]		6362.64	6976.1	613.46
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	6834.54	7590.49	1.11061
797	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]	Subtracted	6362.64	6976.1	613.46
798	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	Divided	6834.54	7590.49	1.11061
799	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Subtracted	5222.71	5834.57	611.86
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	6834.54	7590.49	1.11061
800	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Subtracted	3583.56	4194.95	611.39
	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	Divided	6075.55	6746.92	1.1105

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.