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 577 to 626 of 3730 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
289	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	0	15147.2	14091.9	1.07489
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	1	272.781	246.892	1.10486
290	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	0	15147.2	14091.9	1.07489
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	1	231.969	210.064	1.10428
291	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	0	10922.9	11731.8	1.07406
	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]	1	251.679	228.037	1.10368
292	40s ribosomal protein s15a. [swissprot;acc:p39027]		241.411	266.414	1.10357
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	0	10280.5	9574.98	1.07368
293	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	1	240.782	265.717	1.10356
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	0	10287.1	9583.27	1.07344
294	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]	1	240.782	265.717	1.10356
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	0	13981.5	13025.1	1.07343
295	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	1	223.273	202.423	1.103
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	0	13687.7	12751.8	1.07339
296	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]		10194.1	10941.8	1.07335
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	1	241.282	266.12	1.10294
297	60s ribosomal protein l7. [swissprot;acc:p18124]		235.727	259.984	1.1029
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	0	8123.75	8719	1.07327
298	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]		11977.8	12842.5	1.07219
	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]	1	268.632	243.588	1.10281
299	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0	12338.7	11512.3	1.07178
	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	1	268.635	243.592	1.10281
300	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	0	9270.49	8650.24	1.0717
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	1	150.959	166.351	1.10196
301	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]		150.982	166.372	1.10193
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	0	12783	13698	1.07158
302	60s ribosomal protein l26. [swissprot;acc:q02877]	1	242.326	267.008	1.10185
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	0	7386.71	6895.44	1.07125
303	60s ribosomal protein l35. [swissprot;acc:p42766]	1	242.333	266.999	1.10179
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	0	11431.4	12244.1	1.07109
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	1	242.339	266.986	1.1017
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	0	8021.78	7496.8	1.07003
305	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]		9431	8815	1.06988
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	1	242.339	266.986	1.1017
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		242.153	266.673	1.10126
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	0	5540	5921	1.06877
307	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]		1091	1021	1.06856
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	1	242.153	266.673	1.10126
308	60s ribosomal protein l34. [swissprot;acc:p49207]
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	0	11414.1	12191.8	1.06814
309	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]		13651	14572	1.06747
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	1	242.153	266.673	1.10126
310	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	0	9328.78	8741.55	1.06718
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	1	242.153	266.673	1.10126
311	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	0	10253.5	9622.45	1.06558
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	1	242.627	267.151	1.10108
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]		242.195	266.663	1.10103
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	0	11959.8	12731.1	1.06449
313	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]		11935.6	12698.9	1.06395
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	1	232.473	211.207	1.10069

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.