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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 801 to 850 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
401	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Subtracted	236.224	254.434	18.21
	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	Divided	226.218	207.908	1.08807
402	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Subtracted	249.983	231.802	18.181
	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Divided	226.218	207.908	1.08807
403	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Subtracted	246.338	228.468	17.87
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Divided	226.218	207.908	1.08807
404	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	Subtracted	246.33	228.463	17.867
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Divided	226.218	207.908	1.08807
405	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]		226.209	207.931	1.0879
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Subtracted	83.0461	65.4586	17.5875
406	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		254.667	237.109	17.558
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Divided	244.304	265.634	1.08731
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		260.544	239.75	1.08673
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Subtracted	254.667	237.109	17.558
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Divided	234.804	255.112	1.08649
	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	Subtracted	254.667	237.109	17.558
409	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Divided	261.874	241.045	1.08641
	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	Subtracted	254.667	237.109	17.558
410	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Divided	253.539	233.376	1.0864
411	60s ribosomal protein l18. [swissprot;acc:q07020]	Subtracted	254.667	237.109	17.558
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Divided	253.539	233.376	1.0864
412	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Subtracted	234.547	251.926	17.379
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Divided	261.416	240.788	1.08567
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]		261.45	240.913	1.08525
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Subtracted	205.9	223.202	17.302
414	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Divided	252.238	232.431	1.08522
	max protein. [swissprot;acc:p25912]	Subtracted	210.561	227.828	17.267
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Divided	252.166	232.382	1.08514
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Subtracted	183.423	200.586	17.163
416	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	Divided	261.041	240.6	1.08496
	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Subtracted	183.66	200.791	17.131
417	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Divided	253.197	233.539	1.08417
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Subtracted	218.837	235.94	17.103
418	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Divided	253.197	233.539	1.08417
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Subtracted	216.674	233.723	17.049
419	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Divided	253.197	233.539	1.08417
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Subtracted	218.925	235.922	16.997
420	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Divided	253.197	233.539	1.08417
	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	Subtracted	255.68	238.704	16.976
421	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Divided	205.9	223.202	1.08403
422	ras-related protein rab-37. [swissprot;acc:q96ax2]		260.193	240.287	1.08284
	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	Subtracted	255.68	238.704	16.976
423	oligophrenin 1. [swissprot;acc:o60890]
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Divided	260.193	240.287	1.08284
424	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Subtracted	234.951	251.83	16.879
425	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]		229.411	212.547	16.864
	max protein. [swissprot;acc:p25912]	Divided	210.561	227.828	1.082

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.