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 358 to 407 of 3228 in total

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

Rank	description	red	green	network_comparison
358	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	5061.11	5950.22	1.17567
359	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	12798.9	10887.2	1.17559
360	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	12796.8	10886	1.17553
361	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	12787.6	10880.5	1.17528
362	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	12786.6	10879.9	1.17525
363	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	12780.7	10876.4	1.17509
364	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	5189	6088.47	1.17334
365	calcyphosine. [swissprot;acc:q13938]
366	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
367	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	4024.4	4719.35	1.17268
368	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	5082.66	5959.99	1.17261
369	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	3583.56	4194.95	1.17061
370	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	4108.15	4808.93	1.17058
371	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	5067.02	5926.46	1.16961
372	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	5067	5926.17	1.16956
373	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	5066.99	5926.1	1.16955
374	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	5066.93	5925.38	1.16942
375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	4700.42	5492.63	1.16854
376	44050 protein. [refseq;acc:nm_178832]	17385.9	14889.2	1.16769
377	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]
378	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	12471.7	14561.7	1.16758
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	6704.44	7811.45	1.16512
380	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	12998.5	15138.2	1.16461
381	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	5246.01	6109.31	1.16456
382	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	4533.74	5279.4	1.16447
383	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
384	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
385	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]
386	60s ribosomal protein l8. [swissprot;acc:p25120]
387	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]
390	rw1 protein (fragment). [swissprot;acc:q92545]
391	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	3658.76	3144.39	1.16358
392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	3641.89	4236.95	1.16339
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	4490.28	5222.25	1.16301
394	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]
395	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	4532.73	5269.33	1.16251
396	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	6563.65	7627.29	1.16205
397	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	5367.04	6233.12	1.16137
398	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	5084.26	5904.1	1.16125
399	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	5201.41	4479.76	1.16109
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]
402	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]
403	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
404	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]
405	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
406	thymic stromal co-transporter. [refseq;acc:nm_033051]
407	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	6603.41	7664.65	1.16071

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.