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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 818 to 867 of 6456 in total 
    Value Type	Ranked
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Network Comparison Type	red	green	network_comparison	
409	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	Subtracted	237.109	254.667	17.558	
410	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	Subtracted	237.109	254.667	17.558	
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]	Divided	233.376	253.539	1.0864	
411	60s ribosomal protein l18. [source:swissprot;acc:q07020]	Subtracted	237.109	254.667	17.558	
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]	Divided	233.376	253.539	1.0864	
412	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Subtracted	251.926	234.547	17.379	
412	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	Divided	240.788	261.416	1.08567	
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	Divided	240.913	261.45	1.08525	
413	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Subtracted	223.202	205.9	17.302	
414	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	Divided	232.431	252.238	1.08522	
414	max protein. [source:swissprot;acc:p25912]	Subtracted	227.828	210.561	17.267	
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	Divided	232.382	252.166	1.08514	
415	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	Subtracted	200.586	183.423	17.163	
416	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	Divided	240.6	261.041	1.08496	
416	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]	Subtracted	200.791	183.66	17.131	
417	set domain and mariner transposase fusion gene. [source:refseq;acc:nm_006515]	Divided	233.539	253.197	1.08417	
417	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Subtracted	235.94	218.837	17.103	
418	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	Divided	233.539	253.197	1.08417	
418	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	Subtracted	233.723	216.674	17.049	
419	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	Divided	233.539	253.197	1.08417	
419	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Subtracted	235.922	218.925	16.997	
420	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [source:refseq;acc:nm_021155]	Divided	233.539	253.197	1.08417	
420	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	Subtracted	238.704	255.68	16.976	
421	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	Subtracted	238.704	255.68	16.976	
421	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Divided	223.202	205.9	1.08403	
422	ras-related protein rab-37. [source:swissprot;acc:q96ax2]	Divided	240.287	260.193	1.08284	
422	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	Subtracted	238.704	255.68	16.976	
423	oligophrenin 1. [source:swissprot;acc:o60890]	Subtracted	238.704	255.68	16.976	
423	ras-related protein rab-26. [source:swissprot;acc:q9ulw5]	Divided	240.287	260.193	1.08284	
424	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [source:swissprot;acc:p19387]	Divided	240.287	260.193	1.08284	
424	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	Subtracted	251.83	234.951	16.879	
425	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [source:swissprot;acc:q14249]	Subtracted	212.547	229.411	16.864	
425	max protein. [source:swissprot;acc:p25912]	Divided	227.828	210.561	1.082	
426	dynactin 4. [source:refseq;acc:nm_032486]	Divided	233.142	252.253	1.08197	
426	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [source:swissprot;acc:o95831]	Subtracted	212.547	229.411	16.864	
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	Divided	239.977	259.525	1.08146	
427	t-box transcription factor tbx6 (t-box protein 6). [source:swissprot;acc:o95947]	Subtracted	212.547	229.411	16.864	
428	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Divided	253.852	234.808	1.0811	
428	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Subtracted	227.748	210.888	16.86	
429	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	Divided	239.709	259.038	1.08064	
429	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	Subtracted	251.344	234.514	16.83	
430	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	Subtracted	250.938	234.134	16.804	
430	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Divided	227.748	210.888	1.07995	
431	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	Subtracted	233.529	216.737	16.792	
431	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	Divided	236.245	255.113	1.07987	
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [source:swissprot;acc:q14249]	Divided	212.547	229.411	1.07934	
432	mct-1 protein. [source:refseq;acc:nm_014060]	Subtracted	226.313	243.03	16.717	
433	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	Subtracted	226.313	243.03	16.717	
433	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [source:swissprot;acc:o95831]	Divided	212.547	229.411	1.07934	
434	ad24 protein. [source:refseq;acc:nm_022451]	Subtracted	251.334	234.672	16.662	

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/