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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 368 to 417 of 3228 in total

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

Rank	green	red	description	network_comparison
368	265.715	242.66	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	1.09501
369	265.104	242.159	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	1.09475
370			nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
371	170.42	186.52	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	1.09447
372			ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
373	265.255	242.37	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	1.09442
374	244.168	267.208	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	1.09436
375	265.516	242.686	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	1.09407
376	234.945	257.017	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	1.09395
377	265.481	242.691	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	1.09391
378	265.365	242.593	60s ribosomal protein l30. [swissprot;acc:p04645]	1.09387
379	264.163	241.509	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	1.0938
380	264.79	242.109	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	1.09368
381	183.423	200.586	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	1.09357
382	183.66	200.791	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
383	217.739	237.862	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	1.09242
384	244.236	266.421	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
385			transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386	264.11	242.238	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	1.09029
387			40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
388	208.756	227.575	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1.09015
389			small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
390	263.62	241.828	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	1.09011
391			40s ribosomal protein s16. [swissprot;acc:p17008]
392	263.615	241.83	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	1.09008
393	207.072	225.719	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	1.09005
394	238.407	218.827	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	1.08948
395			dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
396	262.34	240.801	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	1.08945
397	101.613	110.689	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	1.08932
398	238.358	218.818	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	1.0893
399	226.226	207.889	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	1.08821
400	226.218	207.908	phosducin-like protein (phlp). [swissprot;acc:q13371]	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	226.209	207.931	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	1.0879
406	244.304	265.634	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	1.08731
407	260.544	239.75	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	1.08673
408	234.804	255.112	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	1.08649
409	261.874	241.045	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	1.08641
410	253.539	233.376	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
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	240.788	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	1.08567
413	261.45	240.913	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	1.08525
414	252.238	232.431	katanin p60 subunit a 1. [refseq;acc:nm_007044]	1.08522
415	252.166	232.382	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	1.08514
416	261.041	240.6	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	1.08496
417	253.197	233.539	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	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.