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 368 to 417 of 3228 in total

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

Rank	description	red	green	network_comparison
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	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
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	186.52	170.42	1.09447
372	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	242.37	265.255	1.09442
374	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	267.208	244.168	1.09436
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	242.686	265.516	1.09407
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	257.017	234.945	1.09395
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	242.691	265.481	1.09391
378	60s ribosomal protein l30. [swissprot;acc:p04645]	242.593	265.365	1.09387
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	241.509	264.163	1.0938
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	264.79	1.09368
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	200.586	183.423	1.09357
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]	200.791	183.66	1.09328
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	237.862	217.739	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]	266.421	244.236	1.09083
385	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
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

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.