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 332 to 381 of 3228 in total

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

Rank	description	red	green	network_comparison
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	5051.16	5975.51	1.183
333	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	5039.63	5961.83	1.18299
334	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	14924.4	17655.2	1.18298
335	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	3494.31	4129.6	1.18181
336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	3751.3	4431.34	1.18128
337	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	20446.1	24136.4	1.18049
338	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]
339	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]
340	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
341	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]
342	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
343	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
344	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
345	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
346	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	14229.2	16780.7	1.17931
347	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	4991.02	5885.09	1.17914
348	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]
349	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	4714.85	5554.38	1.17806
350	sedlin. [swissprot;acc:o14582]	17396.9	20483.9	1.17745
351	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
352	bet3 homolog. [swissprot;acc:o43617]
353	p66 alpha. [refseq;acc:nm_017660]	12839	10911.1	1.17669
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	12944.2	1.1763
357	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	5061.11	5950.22	1.17567
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	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

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.