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 3408 to 3457 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
213	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	Squared	Divided	1	86861.5	65369.7	1.32877
214	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Measured	Subtracted	0	1217.92	1367.83	149.91
	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Rooted		1	121.695	131.815	10.12
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Ranked	Divided		191.644	170.192	1.12605
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Measured	Subtracted		7711.36	6265.79	1445.57
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	Ranked			241.282	266.12	24.838
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Squared	Divided	0	98.1677	70.141	1.39958
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]		Subtracted	1	28994.2	17134.8	11859.4
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Rooted		0	34.7164	32.0874	2.629
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Ranked	Divided		7621.99	8473.85	1.11176
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Rooted		1	105.205	92.2415	1.14054
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Measured		0	13174.7	15605.1	1.18447
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Squared	Subtracted		634.375	361.911	272.464
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Rooted	Divided		21.5042	18.9231	1.1364
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Squared		1	52591.3	69845.1	1.32807
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Ranked	Subtracted	0	14898.9	16041.6	1142.7
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Measured	Divided	1	4074.83	5086.49	1.24827
215	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]		Subtracted	0	1658.23	1805.52	147.29
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Rooted	Divided	1	105.205	92.2415	1.14054
	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]			0	9.36926	8.24639	1.13617
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Ranked	Subtracted	1	237.292	212.457	24.835
	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	Rooted		0	24.8155	27.4116	2.5961
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]			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

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.