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

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Showing element 351 to 400 of 3228 in total

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

Rank	description	red	network_comparison	green
351	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	17396.9	1.17745	20483.9
352	bet3 homolog. [swissprot;acc:o43617]
353	p66 alpha. [refseq;acc:nm_017660]	12839	1.17669	10911.1
354	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]
355	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
356	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	11004.2	1.1763	12944.2
357	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	5061.11	1.17567	5950.22
358	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]
359	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	12798.9	1.17559	10887.2
360	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	12796.8	1.17553	10886
361	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	12787.6	1.17528	10880.5
362	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	12786.6	1.17525	10879.9
363	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	12780.7	1.17509	10876.4
364	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	5189	1.17334	6088.47
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	1.17268	4719.35
368	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	5082.66	1.17261	5959.99
369	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	3583.56	1.17061	4194.95
370	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	4108.15	1.17058	4808.93
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	1.16961	5926.46
372	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	5067	1.16956	5926.17
373	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	5066.99	1.16955	5926.1
374	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	5066.93	1.16942	5925.38
375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	4700.42	1.16854	5492.63
376	44050 protein. [refseq;acc:nm_178832]	17385.9	1.16769	14889.2
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	1.16758	14561.7
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	6704.44	1.16512	7811.45
380	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	12998.5	1.16461	15138.2
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	1.16456	6109.31
382	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	4533.74	1.16447	5279.4
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	1.16358	3144.39
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	1.16339	4236.95
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	4490.28	1.16301	5222.25
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	1.16251	5269.33
396	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	6563.65	1.16205	7627.29
397	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	5367.04	1.16137	6233.12
398	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	5084.26	1.16125	5904.1
399	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	5201.41	1.16109	4479.76
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]

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.