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 694 to 743 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
347	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Subtracted	231.481	211.131	20.35
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Divided	242.14	265.696	1.09728
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Subtracted	185.969	165.623	20.346
349	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]		255.112	234.804	20.308
	surfeit locus protein 5. [swissprot;acc:q15528]	Divided	242.14	265.696	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	233.376	253.539	20.163
	zinc finger protein 291. [swissprot;acc:q9by12]	Divided	242.14	265.696	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	233.376	253.539	20.163
352	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	Divided	242.14	265.696	1.09728
	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	Subtracted	237.862	217.739	20.123
353	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]		94	114	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	231.73	211.252	1.09694
354	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Subtracted	94	114	20
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Divided	234.691	257.442	1.09694
355	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Subtracted	94	114	20
	syntaxin 6. [swissprot;acc:o43752]	Divided	234.673	257.414	1.09691
356	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]		243.24	266.796	1.09684
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Subtracted	94	114	20
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

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.