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

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Showing element 382 to 431 of 3228 in total

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

Rank	green	description	network_comparison	red
382	183.66	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]	1.09328	200.791
383	217.739	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	1.09242	237.862
384	244.236	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]	1.09083	266.421
385		transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386	264.11	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	1.09029	242.238
387		40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
388	208.756	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1.09015	227.575
389		small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
390	263.62	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	1.09011	241.828
391		40s ribosomal protein s16. [swissprot;acc:p17008]
392	263.615	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	1.09008	241.83
393	207.072	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	1.09005	225.719
394	238.407	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	1.08948	218.827
395		dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
396	262.34	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	1.08945	240.801
397	101.613	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	1.08932	110.689
398	238.358	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	1.0893	218.818
399	226.226	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	1.08821	207.889
400	226.218	phosducin-like protein (phlp). [swissprot;acc:q13371]	1.08807	207.908
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	226.209	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	1.0879	207.931
406	244.304	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	1.08731	265.634
407	260.544	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	1.08673	239.75
408	234.804	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	1.08649	255.112
409	261.874	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	1.08641	241.045
410	253.539	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]	1.0864	233.376
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	261.416	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	1.08567	240.788
413	261.45	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	1.08525	240.913
414	252.238	katanin p60 subunit a 1. [refseq;acc:nm_007044]	1.08522	232.431
415	252.166	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	1.08514	232.382
416	261.041	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	1.08496	240.6
417	253.197	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	1.08417	233.539
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	205.9	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	1.08403	223.202
422	260.193	ras-related protein rab-37. [swissprot;acc:q96ax2]	1.08284	240.287
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	210.561	max protein. [swissprot;acc:p25912]	1.082	227.828
426	252.253	dynactin 4. [refseq;acc:nm_032486]	1.08197	233.142
427	259.525	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	1.08146	239.977
428	234.808	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	1.0811	253.852
429	259.038	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	1.08064	239.709
430	210.888	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	1.07995	227.748
431	255.113	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	1.07987	236.245

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.