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 727 to 776 of 6456 in total 
    Value Type	Ranked
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Network Comparison Type	red	green	network_comparison	
364	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	Subtracted	233.539	253.197	19.658	
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Divided	243.208	266.617	1.09625	
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	Divided	242.744	266.07	1.09609	
365	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	Subtracted	233.539	253.197	19.658	
366	40s ribosomal protein s5. [source:swissprot;acc:p46782]	Divided	242.473	265.756	1.09602	
366	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [source:refseq;acc:nm_021155]	Subtracted	233.539	253.197	19.658	
367	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	Subtracted	218.827	238.407	19.58	
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	Divided	234.146	256.627	1.09601	
368	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	Subtracted	218.827	238.407	19.58	
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	Divided	242.66	265.715	1.09501	
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	Divided	242.159	265.104	1.09475	
369	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	Subtracted	239.977	259.525	19.548	
370	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Subtracted	218.818	238.358	19.54	
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Divided	242.159	265.104	1.09475	
371	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Subtracted	186.172	166.661	19.511	
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Divided	186.52	170.42	1.09447	
372	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	Subtracted	239.709	259.038	19.329	
372	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Divided	186.52	170.42	1.09447	
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Divided	242.37	265.255	1.09442	
373	dynactin 4. [source:refseq;acc:nm_032486]	Subtracted	233.142	252.253	19.111	
374	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Subtracted	248.152	267.226	19.074	
374	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Divided	267.208	244.168	1.09436	
375	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Subtracted	248.152	267.226	19.074	
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	Divided	242.686	265.516	1.09407	
376	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Subtracted	248.152	267.226	19.074	
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Divided	257.017	234.945	1.09395	
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	Divided	242.691	265.481	1.09391	
377	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Subtracted	248.152	267.226	19.074	
378	60s ribosomal protein l30. [source:swissprot;acc:p04645]	Divided	242.593	265.365	1.09387	
378	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Subtracted	248.152	267.226	19.074	
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	Divided	241.509	264.163	1.0938	
379	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Subtracted	248.152	267.226	19.074	
380	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Subtracted	248.152	267.226	19.074	
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Divided	242.109	264.79	1.09368	
381	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Subtracted	248.152	267.226	19.074	
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	Divided	200.586	183.423	1.09357	
382	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Subtracted	253.852	234.808	19.044	
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]	Divided	200.791	183.66	1.09328	
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	Divided	237.862	217.739	1.09242	
383	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	Subtracted	236.245	255.113	18.868	
384	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Subtracted	227.575	208.756	18.819	
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]	Divided	266.421	244.236	1.09083	
385	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Subtracted	227.575	208.756	18.819	
385	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Divided	266.421	244.236	1.09083	
386	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	Divided	242.238	264.11	1.09029	
386	40s ribosomal protein s9. [source:swissprot;acc:p46781]	Subtracted	238.986	257.784	18.798	
387	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	Divided	242.238	264.11	1.09029	
387	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Subtracted	56.6768	75.3531	18.6763	
388	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Subtracted	56.7244	75.3948	18.6704	
388	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Divided	227.575	208.756	1.09015	

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/