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 3430 to 3479 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
215	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Rooted	Subtracted	1	121.695	131.815	10.12
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Ranked	Divided		112	126	1.125
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Squared		0	98.1677	70.141	1.39958
	myosin vi. [swissprot;acc:q9um54]	Ranked			10121.5	11250.5	1.11154
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Measured	Subtracted	1	7711.31	6265.76	1445.55
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Squared			28994.2	17134.8	11859.4
	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723]		Divided		86609.4	65234.5	1.32766
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]		Subtracted	0	492.157	225.924	266.233
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Ranked			7955.61	6817.49	1138.12
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Measured	Divided	1	16074	12888.4	1.24717
	zinc finger protein 277. [swissprot;acc:q9nrm2]			0	13174.7	15605.1	1.18447
216	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]				12478	14756	1.18256
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Rooted			9.36926	8.24639	1.13617
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Measured	Subtracted		1658.07	1805.36	147.29
	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]			1	10067.9	11511	1443.1
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	Ranked		0	5677.96	4546.87	1131.09
	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Squared	Divided		9.56237	6.91035	1.38378
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Rooted	Subtracted	1	121.695	131.815	10.12
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Squared			46785.7	58383.2	11597.5
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Measured	Divided		16071.6	12886.8	1.24714
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Ranked		0	10559.7	11732	1.11102
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]			1	112	126	1.125
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Rooted			105.205	92.2415	1.14054
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	Squared	Subtracted	0	492.157	225.924	266.233
	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]		Divided	1	86600.9	65229.9	1.32763
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Ranked	Subtracted		226.471	201.769	24.702
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Rooted		0	21.5042	18.9231	2.5811
217	40s ribosomal protein s29. [swissprot;acc:p30054]				26.1023	28.6733	2.571
	60s ribosomal protein l12. [swissprot;acc:p30050]	Measured			1657.78	1805.05	147.27
	60s ribosomal protein l26. [swissprot;acc:q02877]	Ranked		1	242.326	267.008	24.682
	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]		Divided	0	7101.79	6406.18	1.10858
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Rooted			9.37502	8.25148	1.13616
	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	Squared	Subtracted		181.122	444.663	263.541
	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Ranked			5677.89	4547.43	1130.46
	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	Squared		1	46785.7	58383.2	11597.5
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Ranked	Divided		112	126	1.125
	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284]	Squared			86600.9	65229.9	1.32763
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Rooted			105.205	92.2415	1.14054
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	Measured	Subtracted		6417.18	7859.6	1442.42
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]		Divided		16071.6	12886.8	1.24714
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Rooted	Subtracted		121.695	131.815	10.12
	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	Squared	Divided	0	9.56237	6.91035	1.38378
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Measured			903.967	771.309	1.17199
218	60s ribosomal protein l35. [swissprot;acc:p42766]	Ranked	Subtracted	1	242.333	266.999	24.666
	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	Rooted	Divided	0	19.7165	17.3602	1.13573
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Ranked	Subtracted		5677.86	4547.66	1130.2
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Rooted	Divided	1	46.1476	52.5742	1.13926
	kappa b-ras 1. [refseq;acc:nm_020345]	Squared	Subtracted	0	1558.15	1297.17	260.98
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Measured			1225.47	1079.01	146.46
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Ranked	Divided		19355	17469.2	1.10795

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.