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 801 to 850 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	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	254.434	236.224	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	207.908	226.218	1.08807
402	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Subtracted	231.802	249.983	18.181
	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Divided	207.908	226.218	1.08807
403	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Subtracted	228.468	246.338	17.87
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Divided	207.908	226.218	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	228.463	246.33	17.867
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Divided	207.908	226.218	1.08807
405	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]		207.931	226.209	1.0879
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Subtracted	65.4586	83.0461	17.5875
406	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		237.109	254.667	17.558
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Divided	265.634	244.304	1.08731
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		239.75	260.544	1.08673
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Subtracted	237.109	254.667	17.558
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Divided	255.112	234.804	1.08649
	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	Subtracted	237.109	254.667	17.558
409	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Divided	241.045	261.874	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	237.109	254.667	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	233.376	253.539	1.0864
411	60s ribosomal protein l18. [swissprot;acc:q07020]	Subtracted	237.109	254.667	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	233.376	253.539	1.0864
412	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Subtracted	251.926	234.547	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	240.788	261.416	1.08567
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]		240.913	261.45	1.08525
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Subtracted	223.202	205.9	17.302
414	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Divided	232.431	252.238	1.08522
	max protein. [swissprot;acc:p25912]	Subtracted	227.828	210.561	17.267
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Divided	232.382	252.166	1.08514
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Subtracted	200.586	183.423	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	240.6	261.041	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	200.791	183.66	17.131
417	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Divided	233.539	253.197	1.08417
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Subtracted	235.94	218.837	17.103
418	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Divided	233.539	253.197	1.08417
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Subtracted	233.723	216.674	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	233.539	253.197	1.08417
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Subtracted	235.922	218.925	16.997
420	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Divided	233.539	253.197	1.08417
	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	Subtracted	238.704	255.68	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	223.202	205.9	1.08403
422	ras-related protein rab-37. [swissprot;acc:q96ax2]		240.287	260.193	1.08284
	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	Subtracted	238.704	255.68	16.976
423	oligophrenin 1. [swissprot;acc:o60890]
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Divided	240.287	260.193	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	251.83	234.951	16.879
425	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]		212.547	229.411	16.864
	max protein. [swissprot;acc:p25912]	Divided	227.828	210.561	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.