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 4930 to 4979 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2465	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Divided	235.812	235.088	1.00308
2466	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	Subtracted	216.64	217.285	0.645
	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]	Divided	235.812	235.088	1.00308
2467	secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]	Subtracted	204.688	205.333	0.645
	suppressor of fused. [refseq;acc:nm_016169]	Divided	235.812	235.088	1.00308
2468	secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]	Subtracted	204.688	205.333	0.645
	zinc finger protein gli3. [swissprot;acc:p10071]	Divided	235.812	235.088	1.00308
2469	limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]	Subtracted	204.688	205.332	0.644
2470	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]	Divided	235.812	235.088	1.00308
	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4]	Subtracted	204.683	205.326	0.643
2471	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]
	zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]	Divided	235.812	235.088	1.00308
2472	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]	Subtracted	204.683	205.326	0.643
	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748]	Divided	218.218	217.564	1.00301
2473	c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6]		218.644	217.991	1.003
	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183]	Subtracted	204.683	205.326	0.643
2474	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	Divided	216.64	217.285	1.00298
	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903]	Subtracted	204.653	205.286	0.633
2475	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319]	Divided	218.219	217.571	1.00298
	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	Subtracted	211.205	210.577	0.628
2476	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]		218.093	218.72	0.627
	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	Divided	211.205	210.577	1.00298
2477	mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]		216.177	216.801	1.00289
	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960]	Subtracted	218.093	218.72	0.627
2478	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	Divided	216.177	216.801	1.00289
	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]	Subtracted	218.093	218.72	0.627
2479	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]
	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]	Divided			1.00287
2480	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]	Subtracted			0.627
	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960]	Divided			1.00287
2481	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]
	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]	Subtracted			0.627
2482	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]	Divided			1.00287
	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]	Subtracted			0.627
2483	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]	Divided			1.00287
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Subtracted			0.627
2484	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]	Divided			1.00287
2485	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]
	mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]	Subtracted	216.177	216.801	0.624
2486	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Divided	218.093	218.72	1.00287
2487	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Subtracted	218.949	219.552	0.603
	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]	Divided	218.093	218.72	1.00287
2488	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	Subtracted	180.137	180.732	0.595
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Divided	194.527	195.08	1.00284
2489	dc11 protein. [refseq;acc:nm_020186]
	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	Subtracted	182.272	181.683	0.589
2490	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]	Divided	194.527	195.08	1.00284

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.