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

Results: HTML CSV LaTeX

Showing element 4941 to 4990 of 6456 in total

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

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
2471	GLI2	zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]	Divided	235.812	235.088	1.00308
	SLC13A3	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]	Subtracted	204.683	205.326	0.643
2472	SLC13A1	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]
	TNS3	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748]	Divided	218.218	217.564	1.00301
2473	MAPK8IP3	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
	SLC13A2	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	CDS1	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]		204.653	205.286	0.633
	PSMC3	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	Divided	216.64	217.285	1.00298
2475	TENC1	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]		218.219	217.571
	XYLB	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	Subtracted	211.205	210.577	0.628
2476	PRR5	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]		218.093	218.72	0.627
	XYLB	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	Divided	211.205	210.577	1.00298
2477	ARHGAP1	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
	MRPL30	mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]	Divided	216.177	216.801	1.00289
2478	KLC2	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]	Subtracted	218.093	218.72	0.627
	PSMC6	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
2479	KIF5B	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]	Subtracted	218.093	218.72	0.627
	PRR5	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]	Divided			1.00287
2480	ARHGAP1	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960]
	KIF5C	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]	Subtracted			0.627
2481	KIF5A	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]
	KLC2	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]	Divided			1.00287
2482	KIF5B	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]
	KLC1	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]	Subtracted			0.627
2483	GTF3A	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]
	KIF5C	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]	Divided			1.00287
2484	EXOC1	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]	Subtracted			0.627
	KIF5A	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]	Divided			1.00287
2485	KLC1	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]
	MRPL30	mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]	Subtracted	216.177	216.801	0.624
2486	GTF3A	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Divided	218.093	218.72	1.00287
	PSMC6	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	Subtracted	216.177	216.801	0.624
2487	BIRC5	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]		218.949	219.552	0.603
	EXOC1	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]	Divided	218.093	218.72	1.00287
2488	no value	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]		194.527	195.08	1.00284
	ETFA	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	Subtracted	180.137	180.732	0.595
2489	no value	dc11 protein. [refseq;acc:nm_020186]	Divided	194.527	195.08	1.00284
	EPHX1	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	Subtracted	182.272	181.683	0.589
2490	APPBP1	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]	Divided	194.527	195.08	1.00284
	ZMYND8	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4]	Subtracted	217.398	216.809	0.589
2491	ALAS2	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]	Divided	194.527	195.08	1.00284
	ZMYND11	adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326]	Subtracted	217.417	216.844	0.573
2492	GRPEL2	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5]		234.384	234.948	0.564
	UBE1C	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	Divided	194.527	195.08	1.00284
2493	GRPEL1	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]	Subtracted	234.384	234.948	0.564
	UBE1	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]	Divided	194.527	195.08	1.00284
2494	SLC25A12	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
	SMARCD2	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]	Subtracted	234.384	234.948	0.564
2495	HHAT	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	Divided	194.527	195.08	1.00284
	SMARCD3	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]	Subtracted	234.384	234.948	0.564

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
- Hugo is the HGNC identifier if it exists
- 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.