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

Results: HTML CSV LaTeX

Showing element 775 to 824 of 3228 in total

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

Rank	description	red	green	network_comparison
775	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348]	5874.74	6533.33	1.11211
776	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]	5874.76	6533.36
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
778	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]	5874.63	6533.23
779	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]	5874.76	6533.36
780	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]
781	secretory pathway component sec31b-1. [refseq;acc:nm_015490]
782	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]	5874.74	6533.33
783	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]	5874.78	6533.37	1.1121
784	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]	5874.77	6533.36
785	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]	4997	5557.17
786	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	9304.83	10347.3	1.11204
787	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]	5890.49	6547.9	1.11161
788	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]	5890.41	6547.81
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
790	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]	5890.88	6548.28
791	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	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
793	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	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
795	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	6441.14	7154.13	1.11069
796	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	6834.54	7590.49	1.11061
797	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
798	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]
799	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
800	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	6075.55	6746.92	1.1105
801	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	6456.35	7169.75
802	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	6455.66	7168.82	1.11047
803	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	6455.02	7167.96	1.11045
804	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9]	6770.78	7517.97	1.11036
805	60s ribosomal protein l39. [swissprot;acc:p02404]	4708.61	5226.71	1.11003
806	60s ribosomal protein l18a. [swissprot;acc:q02543]
807	40s ribosomal protein s19. [swissprot;acc:p39019]
808	60s ribosomal protein l31. [swissprot;acc:p12947]
809	wd-repeat protein 3. [swissprot;acc:q9unx4]	4039.81	4484.22	1.11001
810	jm1 protein. [refseq;acc:nm_014008]	5794.8	6427.79	1.10923
811	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049]	6000.07	6655.11	1.10917
812	target of myb protein 1. [swissprot;acc:o60784]	5640.79	6255.85	1.10904
813	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]	5641.11	6255.99	1.109
814	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	5641.12
815	midasin (midas-containing protein). [swissprot;acc:q9nu22]	4483.08	4971.62	1.10897
816	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	5641.53	6256.17	1.10895
817	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	6811.2	7547.35	1.10808
818	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	6807.78	7543.28	1.10804
819	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	6805.45	7540.5	1.10801
820	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	6805.86	7540.99
821	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	6257.99	6932.95	1.10786
822	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	6311.6	6989.33	1.10738
823	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	6311.83	6989.6
824	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	5657.53	6263.02	1.10702

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.