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

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Showing element 401 to 450 of 8289 in total

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

Rank	description	Interaction Map	red	green	network_comparison
201	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Low confidence	10392.7	9683.56	1.07323
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	High confidence	4810.22	6075.04	1.26294
202	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]		4812.01	6076.09	1.26269
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Low confidence	10391.8	9682.99	1.0732
203	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	High confidence	11757.8	9352.11	1.25723
	step ii splicing factor slu7. [refseq;acc:nm_006425]	Low confidence	9870.83	10591.9	1.07305
204	carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792]		10374.8	9672.48	1.07261
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	High confidence	4512.19	5655.52	1.25339
205	platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197]	Low confidence	10374.8	9672.51	1.07261
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	High confidence	4512.19	5655.52	1.25339
206	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		5720.25	4577.5	1.24965
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Low confidence	7583.48	8133.08	1.07247
207	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]		9818	10529.5
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	High confidence	4771.21	5961.43	1.24946
208	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Low confidence	6557.13	7028.46	1.07188
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	High confidence	4068.78	5082.18	1.24907
209	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	Low confidence	10348.7	9656.36	1.0717
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	High confidence	4068.78	5082.18	1.24907
210	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Low confidence	9371.08	10040.2	1.0714
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	High confidence	4068.82	5082.21	1.24906
211	bet3 homolog. [swissprot;acc:o43617]	Low confidence	8749.42	9372.33	1.07119
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	High confidence	4068.91	5082.27	1.24905
212	tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184]	Low confidence	6236.57	6679.63	1.07104
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	High confidence	4446.72	5553.79	1.24896
213	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
	putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94]	Low confidence	7777.65	8326.47	1.07056
214	core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156]		10492.4	9804.73	1.07014
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	High confidence	4074.83	5086.49	1.24827
215	neurochondrin. [refseq;acc:nm_014284]	Low confidence	10492.4	9804.73	1.07014
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	High confidence	16074	12888.4	1.24717
216	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]		16071.6	12886.8	1.24714
	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	Low confidence	8973.23	9597.94	1.06962
217	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]		7633.16	8153.06	1.06811
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	High confidence	16071.6	12886.8	1.24714
218	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Low confidence	7266.93	7759.2	1.06774
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	High confidence	16070.4	12886	1.24712
219	transforming protein n-ras. [swissprot;acc:p01111]		16069.8	12885.6	1.24711
	u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012]	Low confidence	7653.44	8171.53	1.06769
220	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	High confidence	41482.5	33356.5	1.24361
	n-acetylglutamate synthase. [refseq;acc:nm_153006]	Low confidence	9395.91	10028.6	1.06734
221	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	High confidence	41482.5	33356.5	1.24361
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Low confidence	10491.4	9831.19	1.06715
222	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	High confidence	41482.5	33356.5	1.24361
	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]	Low confidence	9556.43	10196.2	1.06695
223	cytohesin 4. [swissprot;acc:q9uia0]	High confidence	41482.5	33356.5	1.24361
	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]	Low confidence	7600.32	8107.39	1.06672
224	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	High confidence	41482.5	33356.5	1.24361
	malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298]	Low confidence	6228.87	5839.8	1.06662
225	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	High confidence	9035	7279.6	1.24114
	tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493]	Low confidence	7604	8109.6	1.06649

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.