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

Results: HTML CSV LaTeX

Showing element 1158 to 1207 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	red	green	network_comparison
290	Ranked	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	231.969	210.064	1.10428
	Squared	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	15734.4	20126.8	1.27916
	Rooted	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	75.6323	67.6572	1.11788
291	Measured	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	44490.5	36927.5	1.20481
	Ranked	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	251.679	228.037	1.10368
	Squared	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	59016.1	75486.9	1.27909
	Rooted	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	113.983	101.979	1.11771
292	Measured	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	4641.09	5588.75	1.20419
	Ranked	40s ribosomal protein s15a. [swissprot;acc:p39027]	241.411	266.414	1.10357
	Squared	neuralized-like. [refseq;acc:nm_004210]	6828.26	8728.66	1.27831
	Rooted	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	56.48	63.119	1.11755
293	Measured	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	4641.09	5588.75	1.20419
	Ranked	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	240.782	265.717	1.10356
	Squared	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	35991.8	46002.9	1.27815
	Rooted	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	63.0715	56.4506	1.11729
294	Measured	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	22515.5	18702.6	1.20387
	Ranked	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	240.782	265.717	1.10356
	Squared	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	30826.5	39383.9	1.2776
	Rooted	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	59.0296	65.951	1.11725
295	Measured	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	13261.9	11017.8	1.20368
	Ranked	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	223.273	202.423	1.103
	Squared	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	30807.7	39351.7	1.27733
	Rooted	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	59.029	65.9421	1.11711
296	Measured	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	4911.81	5909.18	1.20306
	Ranked	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	241.282	266.12	1.10294
	Squared	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	28878.8	36783.5	1.27372
	Rooted	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	63.0663	56.4667	1.11688
297	Measured	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	4911.81	5909.18	1.20306
	Ranked	60s ribosomal protein l7. [swissprot;acc:p18124]	235.727	259.984	1.1029
	Squared	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	14247.4	18142.1	1.27336
	Rooted	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	63.0663	56.4667	1.11688
298	Measured	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	4633.92	5572.85	1.20262
	Ranked	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	268.632	243.588	1.10281
	Squared	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	14247.4	18142.1	1.27336
	Rooted	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	57.6823	64.4212	1.11683
299	Measured	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	4914.27	5907.12	1.20203
	Ranked	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	268.635	243.592	1.10281
	Squared	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	28896.2	36767	1.27238
	Rooted	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	59.026	65.8955	1.11638
300	Measured	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	4914.27	5907.12	1.20203
	Ranked	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	150.959	166.351	1.10196
	Squared	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	28896.2	36767	1.27238
	Rooted	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	48.1584	53.7378	1.11586
301	Measured	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	13768.2	11466	1.20078
	Ranked	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	150.982	166.372	1.10193
	Squared	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	28896.2	36767	1.27238
	Rooted	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]	203.673	182.638	1.11517
302	Measured	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	5894.75	7073.65	1.19999
	Ranked	60s ribosomal protein l26. [swissprot;acc:q02877]	242.326	267.008	1.10185
	Squared	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	28896.2	36767	1.27238

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.