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 713 to 762 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Divided	243.12	266.661	1.09683
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Subtracted	94	114	20
358	ras-related protein rab-37. [swissprot;acc:q96ax2]		240.287	260.193	19.906
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Divided	243.12	266.662	1.09683
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]		239.277	262.434	1.09678
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Subtracted	240.287	260.193	19.906
360	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Divided	243.072	266.559	1.09663
361	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Subtracted	232.431	252.238	19.807
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Divided	242.83	266.248	1.09644
362	apical-like protein (apxl protein). [swissprot;acc:q13796]		231.492	211.136	1.09641
	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Subtracted	232.382	252.166	19.784
363	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]		233.539	253.197	19.658
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Divided	231.481	211.131	1.09639
364	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Subtracted	233.539	253.197	19.658
	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Divided	243.208	266.617	1.09625
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]		242.744	266.07	1.09609
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Subtracted	233.539	253.197	19.658
366	40s ribosomal protein s5. [swissprot;acc:p46782]	Divided	242.473	265.756	1.09602
	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Subtracted	233.539	253.197	19.658
367	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]		218.827	238.407	19.58
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Divided	234.146	256.627	1.09601
368	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Subtracted	218.827	238.407	19.58
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	Divided	242.66	265.715	1.09501
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]		242.159	265.104	1.09475
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Subtracted	239.977	259.525	19.548
370	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]		218.818	238.358	19.54
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	Divided	242.159	265.104	1.09475
371	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Subtracted	186.172	166.661	19.511
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Divided	186.52	170.42	1.09447
372	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Subtracted	239.709	259.038	19.329
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Divided	186.52	170.42	1.09447
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]		242.37	265.255	1.09442
	dynactin 4. [refseq;acc:nm_032486]	Subtracted	233.142	252.253	19.111
374	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]		248.152	267.226	19.074
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Divided	267.208	244.168	1.09436
375	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Subtracted	248.152	267.226	19.074
	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	Divided	242.686	265.516	1.09407
376	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Subtracted	248.152	267.226	19.074
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Divided	257.017	234.945	1.09395
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]		242.691	265.481	1.09391
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Subtracted	248.152	267.226	19.074
378	60s ribosomal protein l30. [swissprot;acc:p04645]	Divided	242.593	265.365	1.09387
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Subtracted	248.152	267.226	19.074
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	Divided	241.509	264.163	1.0938
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Subtracted	248.152	267.226	19.074
380	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Divided	242.109	264.79	1.09368
381	thymic stromal co-transporter. [refseq;acc:nm_033051]	Subtracted	248.152	267.226	19.074
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Divided	200.586	183.423	1.09357

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.