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 683 to 732 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
342	40s ribosomal protein s20. [swissprot;acc:p17075]	Divided	267.21	243.5	1.09737
	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	Subtracted	261.45	240.913	20.537
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Divided	265.136	241.625	1.0973
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Subtracted	211.252	231.73	20.478
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Divided	265.136	241.625	1.0973
	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	Subtracted	261.041	240.6	20.441
345	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]		204.044	224.445	20.401
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Divided	265.697	242.14	1.09729
346	40s ribosomal protein s3. [swissprot;acc:p23396]		265.119	241.612
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Subtracted	211.136	231.492	20.356
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	Divided	265.697	242.14	1.09729
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Subtracted	211.131	231.481	20.35
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Divided	265.696	242.14	1.09728
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Subtracted	165.623	185.969	20.346
349	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]		234.804	255.112	20.308
	surfeit locus protein 5. [swissprot;acc:q15528]	Divided	265.696	242.14	1.09728
350	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]	Subtracted	253.539	233.376	20.163
	zinc finger protein 291. [swissprot;acc:q9by12]	Divided	265.696	242.14	1.09728
351	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Subtracted	253.539	233.376	20.163
352	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	Divided	265.696	242.14	1.09728
	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	Subtracted	217.739	237.862	20.123
353	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]		114	94	20
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Divided	211.252	231.73	1.09694
354	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Subtracted	114	94	20
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Divided	257.442	234.691	1.09694
355	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Subtracted	114	94	20
	syntaxin 6. [swissprot;acc:o43752]	Divided	257.414	234.673	1.09691
356	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]		266.796	243.24	1.09684
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Subtracted	114	94	20
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Divided	266.661	243.12	1.09683
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Subtracted	114	94	20
358	ras-related protein rab-37. [swissprot;acc:q96ax2]		260.193	240.287	19.906
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Divided	266.662	243.12	1.09683
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]		262.434	239.277	1.09678
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Subtracted	260.193	240.287	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	266.559	243.072	1.09663
361	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Subtracted	252.238	232.431	19.807
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Divided	266.248	242.83	1.09644
362	apical-like protein (apxl protein). [swissprot;acc:q13796]		211.136	231.492	1.09641
	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Subtracted	252.166	232.382	19.784
363	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]		253.197	233.539	19.658
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Divided	211.131	231.481	1.09639
364	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Subtracted	253.197	233.539	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	266.617	243.208	1.09625
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]		266.07	242.744	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	253.197	233.539	19.658
366	40s ribosomal protein s5. [swissprot;acc:p46782]	Divided	265.756	242.473	1.09602
	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Subtracted	253.197	233.539	19.658

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.