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 401 to 450 of 3228 in total

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

Rank	description	red	green	network_comparison	
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	226.218	1.08807	
402	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	207.908	226.218	1.08807	
403	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	207.908	226.218	1.08807	
404	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	207.908	226.218	1.08807	
405	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	207.931	226.209	1.0879	
406	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	265.634	244.304	1.08731	
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	239.75	260.544	1.08673	
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	255.112	234.804	1.08649	
409	rna polymerase i associated factor 53. [source: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). [source: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). [source:swissprot;acc:p32780]	233.376	253.539	1.0864	
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	261.416	1.08567	
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	240.913	261.45	1.08525	
414	katanin p60 subunit a 1. [source: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. [source: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). [source:swissprot;acc:q9h9y6]	240.6	261.041	1.08496	
417	set domain and mariner transposase fusion gene. [source:refseq;acc:nm_006515]	233.539	253.197	1.08417	
418	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	233.539	253.197	1.08417	
419	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	233.539	253.197	1.08417	
420	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [source:refseq;acc:nm_021155]	233.539	253.197	1.08417	
421	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	223.202	205.9	1.08403	
422	ras-related protein rab-37. [source:swissprot;acc:q96ax2]	240.287	260.193	1.08284	
423	ras-related protein rab-26. [source:swissprot;acc:q9ulw5]	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]	240.287	260.193	1.08284	
425	max protein. [source:swissprot;acc:p25912]	227.828	210.561	1.082	
426	dynactin 4. [source:refseq;acc:nm_032486]	233.142	252.253	1.08197	
427	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	239.977	259.525	1.08146	
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]	253.852	234.808	1.0811	
429	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	239.709	259.038	1.08064	
430	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	227.748	210.888	1.07995	
431	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	236.245	255.113	1.07987	
432	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [source:swissprot;acc:q14249]	212.547	229.411	1.07934	
433	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [source:swissprot;acc:o95831]	212.547	229.411	1.07934	
434	t-box transcription factor tbx6 (t-box protein 6). [source:swissprot;acc:o95947]	212.547	229.411	1.07934	
435	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	221.522	205.286	1.07909	
436	paxillin. [source:swissprot;acc:p49023]	221.522	205.286	1.07909	
437	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [source:swissprot;acc:q15642]	209.921	226.459	1.07878	
438	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	233.723	216.674	1.07869	
439	40s ribosomal protein s9. [source:swissprot;acc:p46781]	238.986	257.784	1.07866	
440	highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	231.802	249.983	1.07843	
441	grb2-related adaptor protein. [source:swissprot;acc:q13588]	223.457	207.222	1.07835	
442	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	223.802	207.55	1.0783	
443	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	223.79	207.539	1.0783	
444	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	223.801	207.549	1.0783	
445	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	223.801	207.549	1.0783	
446	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354]	224.049	207.785	1.07827	
447	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955]	224.049	207.785	1.07827	
448	microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2]	228.468	246.338	1.07822	
449	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [source:swissprot;acc:q03001]	228.463	246.33	1.07821	
450	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	235.94	218.837	1.07815	

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/