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	green	red	network_comparison

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Showing element 363 to 412 of 3228 in total

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

Rank	description	green	red	network_comparison
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	211.131	231.481	1.09639
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	266.617	243.208	1.09625
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	266.07	242.744	1.09609
366	40s ribosomal protein s5. [swissprot;acc:p46782]	265.756	242.473	1.09602
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	256.627	234.146	1.09601
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	265.715	242.66	1.09501
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	265.104	242.159	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]	170.42	186.52	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]	265.255	242.37	1.09442
374	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	244.168	267.208	1.09436
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	265.516	242.686	1.09407
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	234.945	257.017	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]	265.481	242.691	1.09391
378	60s ribosomal protein l30. [swissprot;acc:p04645]	265.365	242.593	1.09387
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	264.163	241.509	1.0938
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	264.79	242.109	1.09368
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	183.423	200.586	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]	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

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.