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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Rank Gene Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1980 to 2029 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	Network Comparison Type	description	Interaction Map	red	green	network_comparison	
495	YME1L1	Subtracted	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [source:refseq;acc:nm_014263]	High confidence	222.146	237.393	15.247	
496		Divided	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [source:swissprot;acc:q9p0u1]	Low confidence	203.117	196.671	1.03278	
496		Subtracted	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	High confidence	235.18	250.419	15.239	
496	PPAN-P2RY11	Divided	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	High confidence	250.938	234.134	1.07177	
496	RNF113A	Subtracted	zinc finger protein 183. [source:swissprot;acc:o15541]	Low confidence	205.192	198.726	6.466	
497	CAPS	Subtracted	calcyphosine. [source:swissprot;acc:q13938]	Low confidence	204.363	197.899	6.464	
497	EBNA1BP2	Divided	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	High confidence	251.344	234.514	1.07177	
497	SART1	Subtracted	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]	High confidence	225.026	209.798	15.228	
497	SF4	Divided	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Low confidence	203.117	196.671	1.03278	
498	ARHGEF6	Divided	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	High confidence	220.161	235.95	1.07172	
498	KIFAP3	Divided	kinesin-associated protein 3 (smg gds-associated protein). [source:swissprot;acc:q92845]	Low confidence	203.117	196.671	1.03278	
498	RCL1	Subtracted	rna 3'-terminal phosphate cyclase-like protein (hspc338). [source:swissprot;acc:q9y2p8]	Low confidence	203.85	197.403	6.447	
498	TLX3	Subtracted	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [source:swissprot;acc:o43711]	High confidence	237.28	252.492	15.212	
499	BARX1	Subtracted	homeobox protein barh-like 1. [source:swissprot;acc:q9hbu1]	High confidence	237.28	252.492	15.212	
499	LIMD1	Subtracted	lim domains containing 1. [source:refseq;acc:nm_014240]	Low confidence	203.117	196.671	6.446	
499	POLI	Divided	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Low confidence	203.167	196.732	1.03271	
499	TPI1	Divided	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	High confidence	231.496	248.048	1.0715	
500		Subtracted	probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [source:swissprot;acc:q9p0u1]	Low confidence	203.117	196.671	6.446	
500	ING2	Divided	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	High confidence	224.662	240.673	1.07127	
500	OPN4	Subtracted	opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	High confidence	237.28	252.492	15.212	
500	RCL1	Divided	rna 3'-terminal phosphate cyclase-like protein (hspc338). [source:swissprot;acc:q9y2p8]	Low confidence	203.85	197.403	1.03266	
501	CAPS	Divided	calcyphosine. [source:swissprot;acc:q13938]	Low confidence	204.363	197.899	1.03266	
501	CYC1	Divided	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	High confidence	238.704	255.68	1.07112	
501	SF4	Subtracted	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Low confidence	203.117	196.671	6.446	
501	TLX2	Subtracted	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	High confidence	237.28	252.492	15.212	
502	ARHGAP26	Divided	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	High confidence	238.704	255.68	1.07112	
502	KIFAP3	Subtracted	kinesin-associated protein 3 (smg gds-associated protein). [source:swissprot;acc:q92845]	Low confidence	203.117	196.671	6.446	
502	SART1	Divided	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]	Low confidence	200.271	193.957	1.03255	
502	TLX1	Subtracted	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	High confidence	237.28	252.492	15.212	
503	FOXO4	Subtracted	putative fork head domain transcription factor afx1 (forkhead box protein o4). [source:swissprot;acc:p98177]	Low confidence	205.157	198.715	6.442	
503	HECTD1	Subtracted	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	High confidence	237.28	252.492	15.212	
503	RGN	Divided	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	High confidence	238.704	255.68	1.07112	
503	USP22	Divided	ubiquitin carboxyl-terminal hydrolase 22 (ec 3.1.2.15) (ubiquitin thiolesterase 22) (ubiquitin-specific processing protease 22) (deubiquitinating enzyme 22) (fragment). [source:swissprot;acc:q9upt9]	Low confidence	207.407	200.869	1.03255	
504		Subtracted	hemoglobin gamma-a and gamma-g chains. [source:swissprot;acc:p02096]	Low confidence	205.157	198.715	6.442	
504	BARX2	Subtracted	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	High confidence	237.28	252.492	15.212	
504	OPHN1	Divided	oligophrenin 1. [source:swissprot;acc:o60890]	High confidence	238.704	255.68	1.07112	
504	RNF113A	Divided	zinc finger protein 183. [source:swissprot;acc:o15541]	Low confidence	205.192	198.726	1.03254	
505	APP	Subtracted	amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [source:swissprot;acc:p05067]	Low confidence	205.157	198.715	6.442	
505	NOC3L	Divided	ad24 protein. [source:refseq;acc:nm_022451]	High confidence	251.334	234.672	1.071	
505	PCNA	Divided	proliferating cell nuclear antigen (pcna) (cyclin). [source:swissprot;acc:p12004]	Low confidence	207.84	201.297	1.0325	
505	ZNF593	Subtracted	zinc finger protein t86. [source:swissprot;acc:o00488]	High confidence	246.805	231.796	15.009	
506	EXOSC4	Subtracted	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	High confidence	215.237	230.07	14.833	
506	FOXO4	Divided	putative fork head domain transcription factor afx1 (forkhead box protein o4). [source:swissprot;acc:p98177]	Low confidence	205.157	198.715	1.03242	
506	ING1	Divided	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	High confidence	224.535	240.476	1.071	
506	TTYH2	Subtracted	tweety homolog 2. [source:refseq;acc:nm_032646]	Low confidence	205.157	198.715	6.442	
507		Divided	hemoglobin gamma-a and gamma-g chains. [source:swissprot;acc:p02096]	Low confidence	205.157	198.715	1.03242	
507	EXOSC2	Subtracted	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	High confidence	215.237	230.07	14.833	
507	HBZ	Subtracted	hemoglobin zeta chain (hbaz). [source:swissprot;acc:p02008]	Low confidence	205.157	198.715	6.442	
507	WDR12	Divided	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	High confidence	251.299	234.729	1.07059	
508		Subtracted	alpha 2 globin. [source:refseq;acc:nm_000517]	Low confidence	205.157	198.715	6.442	

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/