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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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Gene	Value Type	Interaction Map	green	Rank	Filtered	description	Network Comparison Type	red	network_comparison

Results: HTML CSV LaTeX

Showing element 7412 to 7461 of 77072 in total

Value Type  : Measured

Interaction Map	green	Rank	Filtered	description	Network Comparison Type	red	network_comparison
High confidence	24136.4	343	1	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Divided	20446.1	1.18049
		344		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
		345		retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
	24446.3	5	0	histone h4. [swissprot;acc:p02304]	Subtracted	21773.1	2673.2
		271			Divided		1.12278
	24908.5	56	1	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	20911	3997.5
		57		ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]
		58		ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
		59		anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
		319		ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Divided		1.19117
		320		ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]
		321		ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
		322		anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
	27904.5	13		myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Subtracted	21591.5	6313
		14		myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
		15		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
		178		myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Divided		1.29238
		179		myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
		180		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
	28492	7		28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	21185	7307
		8		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
		9		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
		10		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
		11		mitochondrial solute carrier protein. [refseq;acc:nm_145305]
		115		28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Divided		1.34491
		116		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
		117		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
		118		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
		119		mitochondrial solute carrier protein. [refseq;acc:nm_145305]
	30022.4	22	0	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Subtracted	31122	1099.6
		411			Divided		1.03663
	33356.5	1	1	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]	Subtracted	41482.5	8126
		2		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
		3		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
		4		cytohesin 4. [swissprot;acc:q9uia0]
		5		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
		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]	Divided		1.24361
		221		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]
		222		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]
		223		cytohesin 4. [swissprot;acc:q9uia0]
		224		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]
	33457.6	44		deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	28136.5	5321.1
		324			Divided		1.18912
	36927.5	6		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	44490.5	7563
		291			Divided		1.20481
	39485	98	0	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Subtracted	39165	320
		470			Divided		1.00817
	40795.8	12	1	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	34190.9	6604.9
		318			Divided		1.19318
Low confidence	0	170	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	364	364

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.