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

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Showing element 2901 to 2950 of 9634 in total

Filtered  : 1
Network Comparison Type  : Divided
Value Type  : Measured

Rank	description	Interaction Map	green	red	network_comparison
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]	High confidence	6533.23	5874.63	1.11211
779	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]		6533.36	5874.76
	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	Low confidence	8729.16	8379.96	1.04167
780	calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705]		7631.04	7325.81
	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]	High confidence	6533.36	5874.76	1.11211
781	secretory pathway component sec31b-1. [refseq;acc:nm_015490]
	vav proto-oncogene. [swissprot;acc:p15498]	Low confidence	8447.62	8109.84	1.04165
782	putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177]		7852.25	7538.43	1.04163
	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]	High confidence	6533.33	5874.74	1.11211
783	tweety homolog 1; tweety homolog. [refseq;acc:nm_020659]	Low confidence	7852.34	7538.53	1.04163
	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]	High confidence	6533.37	5874.78	1.1121
784	cytoglobin (histoglobin) (hgb) (stellate cell activation-associated protein). [swissprot;acc:q8wwm9]	Low confidence	7852.34	7538.53	1.04163
	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]	High confidence	6533.36	5874.77	1.1121
785	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]		5557.17	4997
	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	Low confidence	7852.24	7538.42	1.04163
786	amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [swissprot;acc:p05067]		7852.27	7538.46
	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	High confidence	10347.3	9304.83	1.11204
787	tweety homolog 2. [refseq;acc:nm_032646]	Low confidence	7852.28	7538.46	1.04163
	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]	High confidence	6547.9	5890.49	1.11161
788	hemoglobin zeta chain (hbaz). [swissprot;acc:p02008]	Low confidence	7852.24	7538.42	1.04163
	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]	High confidence	6547.81	5890.41	1.11161
789	alpha 2 globin. [refseq;acc:nm_000517]	Low confidence	7852.23	7538.41	1.04163
	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]	High confidence	6547.99	5890.59	1.1116
790	forkhead box protein o3a (forkhead in rhabdomyosarcoma-like 1) (af6q21 protein). [swissprot;acc:o43524]	Low confidence	7852.34	7538.53	1.04163
	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]	High confidence	6548.28	5890.88	1.1116
791	amyloid-like protein 1 precursor (aplp) (aplp-1) [contains: c30]. [swissprot;acc:p51693]	Low confidence	7852.25	7538.43	1.04163
	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	High confidence	4474.3	4025.3	1.11154
792	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]		7526.2	6772.75	1.11125
	myoglobin. [swissprot;acc:p02144]	Low confidence	7852.24	7538.42	1.04163
793	hemoglobin theta-1 chain. [swissprot;acc:p09105]		7852.23	7538.41
	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	High confidence	5596.36	5036.92	1.11107
794	amyloid-like protein 2 precursor (amyloid protein homolog) (apph) (cdei-box binding protein) (cdebp). [swissprot;acc:q06481]	Low confidence	7852.34	7538.53	1.04163
	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	High confidence	7154.55	6441.17	1.11075
795	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]		7154.13	6441.14	1.11069
	thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669]	Low confidence	8147.14	7821.82	1.04159
796	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	High confidence	7590.49	6834.54	1.11061
	vav-3 protein. [swissprot;acc:q9ukw4]	Low confidence	8445.65	8108.45	1.04159
797	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	High confidence	7590.49	6834.54	1.11061
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Low confidence	8731.6	8383.16	1.04156
798	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]		8221.03	7893.13	1.04154
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	High confidence	7590.49	6834.54	1.11061
799	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	zinc finger protein 183-like 1. [refseq;acc:nm_178861]	Low confidence	7857	7543.76	1.04152
800	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kda subunit precursor (ec 2.4.1.119) (ribophorin i) (rpn-i). [swissprot;acc:p04843]		8164.84	7839.89	1.04145
	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	High confidence	6746.92	6075.55	1.1105
801	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]		7169.75	6456.35
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Low confidence	8162.73	7837.99	1.04143
802	flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	High confidence	7168.82	6455.66	1.11047
803	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]		7167.96	6455.02	1.11045

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.