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

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Showing element 101 to 150 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	green	red	network_comparison
7	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Rooted	Divided	0	9.43398	0.00001	943398
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Ranked	Subtracted		13216	22286	9070
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared		1	442993	310840	132153
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Rooted			168.796	145.551	23.245
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked			212.554	288.754	76.2
	sedlin. [swissprot;acc:o14582]	Measured	Divided	0	43	0.00001	4300000
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Squared	Subtracted		111762	82802.3	28959.7
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Measured	Divided	1	339.5	1153.5	3.39764
		Squared			27.2805	314.926	11.544
		Rooted			18.4255	33.9632	1.84327
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]		Subtracted	0	49.8523	65.4535	15.6012
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Measured			15605.1	13174.7	2430.4
8	db83 protein. [swissprot;acc:p57088]		Divided	1	339.5	1153.5	3.39764
		Squared			27.2805	314.926	11.544
		Rooted			18.4255	33.9632	1.84327
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	Subtracted		354894	250303	104591
	ero1-like. [refseq;acc:nm_014584]		Divided	0	0.00001	1.59148	159148
		Rooted				9.05539	905539
	hbs1-like. [refseq;acc:nm_006620]	Ranked		1	322	215	1.49767
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Subtracted	0	13216	22286	9070
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]			1	362	288	74
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Rooted		0	56.7758	72.1137	15.3379
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Ranked	Divided		21888	11525	1.89918
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Measured	Subtracted		7500.75	5106.93	2393.82
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]			1	28492	21185	7307
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted			168.796	145.551	23.245
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Measured	Divided	0	43	0.00001	4300000
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Squared	Subtracted		386144	414704	28560
9	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]				170319	195397	25078
	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Measured			14756	12478	2278
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Divided		6410	85	75.4118
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Ranked	Subtracted		13216	22286	9070
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]			1	362	288	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted			168.796	145.551	23.245
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]			0	111.067	126.359	15.292
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured		1	28492	21185	7307
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared			162517	256169	93652
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		Divided	0	0.00001	0.852071	85207.1
		Rooted				7.74597	774597
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured		1	1281.5	398.5	3.21581
		Squared			388.696	37.5863	10.3414
		Rooted			35.798	19.9625	1.79326
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Ranked		0	21888	11525	1.89918
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]			1	309	212	1.45755
10	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Squared	Subtracted	0	155919	176989	21070
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Ranked	Divided		14178.1	7509.39	1.88805
		Rooted	Subtracted		40.2058	54.2583	14.0525
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Squared	Divided		0.823905	0.00001	82390.5
		Rooted			7.68115		768115
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured			6410	85	75.4118

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.