Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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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Gene Rank Network Comparison Type description Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 368 to 417 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	242.66	1.09501	265.715	
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	242.159	1.09475	265.104	
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	242.159	1.09475	265.104	
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	186.52	1.09447	170.42	
372	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	186.52	1.09447	170.42	
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	242.37	1.09442	265.255	
374	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	267.208	1.09436	244.168	
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	242.686	1.09407	265.516	
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	257.017	1.09395	234.945	
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	242.691	1.09391	265.481	
378	60s ribosomal protein l30. [source:swissprot;acc:p04645]	242.593	1.09387	265.365	
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	241.509	1.0938	264.163	
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	242.109	1.09368	264.79	
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	200.586	1.09357	183.423	
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. [source:refseq;acc:nm_024885]	200.791	1.09328	183.66	
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	237.862	1.09242	217.739	
384	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	266.421	1.09083	244.236	
385	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	266.421	1.09083	244.236	
386	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	242.238	1.09029	264.11	
387	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	242.238	1.09029	264.11	
388	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	227.575	1.09015	208.756	
389	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	227.575	1.09015	208.756	
390	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	241.828	1.09011	263.62	
391	40s ribosomal protein s16. [source:swissprot;acc:p17008]	241.828	1.09011	263.62	
392	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	241.83	1.09008	263.615	
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	225.719	1.09005	207.072	
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	218.827	1.08948	238.407	
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	218.827	1.08948	238.407	
396	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	240.801	1.08945	262.34	
397	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	110.689	1.08932	101.613	
398	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	218.818	1.0893	238.358	
399	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	207.889	1.08821	226.226	
400	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	207.908	1.08807	226.218	
401	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [source:swissprot;acc:p27694]	207.908	1.08807	226.218	
402	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	207.908	1.08807	226.218	
403	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	207.908	1.08807	226.218	
404	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	207.908	1.08807	226.218	
405	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	207.931	1.0879	226.209	
406	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	265.634	1.08731	244.304	
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	239.75	1.08673	260.544	
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	255.112	1.08649	234.804	
409	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	241.045	1.08641	261.874	
410	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	233.376	1.0864	253.539	
411	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [source:swissprot;acc:p32780]	233.376	1.0864	253.539	
412	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	240.788	1.08567	261.416	
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	240.913	1.08525	261.45	
414	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	232.431	1.08522	252.238	
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	232.382	1.08514	252.166	
416	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	240.6	1.08496	261.041	
417	set domain and mariner transposase fusion gene. [source:refseq;acc:nm_006515]	233.539	1.08417	253.197	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/