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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 480 to 529 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
480	NETO2	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	237.109	254.667	1.07405	
481	NETO1	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	237.109	254.667	1.07405	
482	HNRNPU	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	237.109	254.667	1.07405	
483	RUNX2	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]	237.109	254.667	1.07405	
484	HNRPUL1	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	237.109	254.667	1.07405	
485	RPL18	60s ribosomal protein l18. [source:swissprot;acc:q07020]	237.109	254.667	1.07405	
486	MCTS1	mct-1 protein. [source:refseq;acc:nm_014060]	226.313	243.03	1.07387	
487	MRPL22	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	226.313	243.03	1.07387	
488	SART1	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	225.026	209.798	1.07258	
489	PPM1B	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	231.276	215.627	1.07257	
490	ARHGEF7	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	220.183	236.015	1.0719	
491	GTPBP4	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	251.83	234.951	1.07184	
492	PAK2	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [source:swissprot;acc:q13177]	220.171	235.979	1.0718	
493	COG5	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	220.172	235.98	1.0718	
494	PAK1	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [source:swissprot;acc:q13153]	220.172	235.98	1.0718	
495	PAK3	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	220.171	235.979	1.0718	
496	PPAN-P2RY11	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	250.938	234.134	1.07177	
497	EBNA1BP2	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	251.344	234.514	1.07177	
498	ARHGEF6	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	220.161	235.95	1.07172	
499	TPI1	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	231.496	248.048	1.0715	
500	ING2	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	224.662	240.673	1.07127	
501	CYC1	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	238.704	255.68	1.07112	
502	ARHGAP26	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	238.704	255.68	1.07112	
503	RGN	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	238.704	255.68	1.07112	
504	OPHN1	oligophrenin 1. [source:swissprot;acc:o60890]	238.704	255.68	1.07112	
505	NOC3L	ad24 protein. [source:refseq;acc:nm_022451]	251.334	234.672	1.071	
506	ING1	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	224.535	240.476	1.071	
507	WDR12	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	251.299	234.729	1.07059	
508	CPA3	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	177.698	190.24	1.07058	
509	CPA6	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	177.698	190.239	1.07057	
510	CPB2	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	177.699	190.24	1.07057	
511	NOL1	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	250.053	233.725	1.06986	
512	BOP1	block of proliferation 1. [source:swissprot;acc:q14137]	250.794	234.433	1.06979	
513	DVL1	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	218.596	204.344	1.06975	
514	DVL2	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	218.613	204.382	1.06963	
515	PES1	pescadillo homolog 1. [source:swissprot;acc:o00541]	251.297	234.941	1.06962	
516	LSM8	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	228.255	213.422	1.0695	
517	MTX2	metaxin 2. [source:swissprot;acc:o75431]	219.537	234.793	1.06949	
518	GNL3	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	250.858	234.563	1.06947	
519	DVL3	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	218.702	204.582	1.06902	
520	SLC35D2	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	214.754	229.565	1.06897	
521	EXOSC4	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	215.237	230.07	1.06891	
522	PLRG1	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	222.893	208.523	1.06891	
523	EXOSC2	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	215.237	230.07	1.06891	
524	EXOSC3	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	215.237	230.07	1.06891	
525	EXOSC5	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	215.237	230.07	1.06891	
526	RRP1	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	250.538	234.401	1.06884	
527	DDX31	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	248.56	232.579	1.06871	
528	YME1L1	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [source:refseq;acc:nm_014263]	222.146	237.393	1.06864	
529	DDX18	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	251.653	235.506	1.06856	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/