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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Interaction Map	Value Type	Rank	Gene	Filtered	description	Network Comparison Type	green	red	network_comparison

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Showing element 382 to 431 of 3228 in total

Interaction Map  : High confidence
Value Type  : Ranked
Filtered  : 1
Network Comparison Type  : Divided

Rank	description	green	red	network_comparison
382	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]	183.66	200.791	1.09328
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	217.739	237.862	1.09242
384	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	244.236	266.421	1.09083
385	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	264.11	242.238	1.09029
387	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
388	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	208.756	227.575	1.09015
389	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
390	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	263.62	241.828	1.09011
391	40s ribosomal protein s16. [swissprot;acc:p17008]
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	263.615	241.83	1.09008
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	207.072	225.719	1.09005
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	238.407	218.827	1.08948
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
396	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	262.34	240.801	1.08945
397	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	101.613	110.689	1.08932
398	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	238.358	218.818	1.0893
399	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	226.226	207.889	1.08821
400	phosducin-like protein (phlp). [swissprot;acc:q13371]	226.218	207.908	1.08807
401	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]
402	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
403	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]
404	dna repair protein rad52 homolog. [swissprot;acc:p43351]
405	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	226.209	207.931	1.0879
406	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	244.304	265.634	1.08731
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	260.544	239.75	1.08673
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	234.804	255.112	1.08649
409	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	261.874	241.045	1.08641
410	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]	253.539	233.376	1.0864
411	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
412	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	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
414	katanin p60 subunit a 1. [refseq;acc:nm_007044]	252.238	232.431	1.08522
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	252.166	232.382	1.08514
416	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	261.041	240.6	1.08496
417	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	253.197	233.539	1.08417
418	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]
419	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
420	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
421	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	205.9	223.202	1.08403
422	ras-related protein rab-37. [swissprot;acc:q96ax2]	260.193	240.287	1.08284
423	ras-related protein rab-26. [swissprot;acc:q9ulw5]
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]
425	max protein. [swissprot;acc:p25912]	210.561	227.828	1.082
426	dynactin 4. [refseq;acc:nm_032486]	252.253	233.142	1.08197
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	259.525	239.977	1.08146
428	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	234.808	253.852	1.0811
429	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	259.038	239.709	1.08064
430	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	210.888	227.748	1.07995
431	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	255.113	236.245	1.07987

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.