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 386 to 435 of 3228 in total

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

Rank	description	red	green	network_comparison
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	242.238	264.11	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]	227.575	208.756	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]	241.828	263.62	1.09011
391	40s ribosomal protein s16. [swissprot;acc:p17008]
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	241.83	263.615	1.09008
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	225.719	207.072	1.09005
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	218.827	238.407	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]	240.801	262.34	1.08945
397	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	110.689	101.613	1.08932
398	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	218.818	238.358	1.0893
399	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	207.889	226.226	1.08821
400	phosducin-like protein (phlp). [swissprot;acc:q13371]	207.908	226.218	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]	207.931	226.209	1.0879
406	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	265.634	244.304	1.08731
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	239.75	260.544	1.08673
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	255.112	234.804	1.08649
409	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	241.045	261.874	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]	233.376	253.539	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]	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
414	katanin p60 subunit a 1. [refseq;acc:nm_007044]	232.431	252.238	1.08522
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	232.382	252.166	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]	240.6	261.041	1.08496
417	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	233.539	253.197	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]	223.202	205.9	1.08403
422	ras-related protein rab-37. [swissprot;acc:q96ax2]	240.287	260.193	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]	227.828	210.561	1.082
426	dynactin 4. [refseq;acc:nm_032486]	233.142	252.253	1.08197
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	239.977	259.525	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]	253.852	234.808	1.0811
429	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	239.709	259.038	1.08064
430	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	227.748	210.888	1.07995
431	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	236.245	255.113	1.07987
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	212.547	229.411	1.07934
433	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
434	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
435	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	221.522	205.286	1.07909

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.