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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1330 to 1379 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
665	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	Subtracted	214.254	202.166	12.088	
666	EIF3I	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	Subtracted	250.465	238.38	12.085	
666	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Divided	229.072	216.576	1.0577	
667		trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Subtracted	250.465	238.38	12.085	
667	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Divided	229.072	216.576	1.0577	
668	ABLIM1	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Divided	229.072	216.576	1.0577	
668	FTSJ3	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Subtracted	244.495	232.419	12.076	
669		presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	Subtracted	232.601	244.534	11.933	
669	SYN1	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Divided	229.072	216.576	1.0577	
670	GNL2	autoantigen ngp-1. [source:swissprot;acc:q13823]	Divided	250.302	236.817	1.05694	
670	RANP1	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	Subtracted	232.601	244.534	11.933	
671		presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Subtracted	232.601	244.534	11.933	
671	NUBP1	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Divided	210.739	199.398	1.05688	
672		dok-like protein. [source:refseq;acc:nm_024872]	Subtracted	216.504	204.622	11.882	
672	NUBP2	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Divided	210.739	199.398	1.05688	
673	CASK	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	Divided	226.497	214.355	1.05664	
673	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Subtracted	216.504	204.622	11.882	
674	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Subtracted	216.504	204.622	11.882	
674	HIF3A	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	Divided	226.497	214.355	1.05664	
675	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Subtracted	216.504	204.622	11.882	
675	SIM1	single-minded homolog 1. [source:swissprot;acc:p81133]	Divided	226.497	214.355	1.05664	
676	MRTO4	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [source:refseq;acc:nm_016183]	Subtracted	245.84	257.636	11.796	
676	POLR2G	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	Divided	232.469	245.613	1.05654	
677	FBL	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	Subtracted	245.246	233.483	11.763	
677	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Divided	228.944	216.745	1.05628	
678	PPIL4	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [source:refseq;acc:nm_139126]	Subtracted	226.135	214.405	11.73	
678	SNX5	sorting nexin 5. [source:swissprot;acc:q9y5x3]	Divided	208.482	220.175	1.05609	
679		homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Divided	132.413	125.389	1.05602	
679	SNX5	sorting nexin 5. [source:swissprot;acc:q9y5x3]	Subtracted	208.482	220.175	11.693	
680	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Divided	132.413	125.389	1.05602	
680	SFRS18	sr rich protein. [source:refseq;acc:nm_032870]	Subtracted	225.293	213.64	11.653	
681	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Divided	132.413	125.389	1.05602	
681	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Subtracted	220.593	208.987	11.606	
682		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Divided	132.413	125.389	1.05602	
682	NAT10	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Subtracted	246.055	234.458	11.597	
683	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Divided	132.413	125.389	1.05602	
683	OSTF1	osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	Subtracted	231.809	243.289	11.48	
684	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Divided	132.413	125.389	1.05602	
684	PFAS	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	Subtracted	223.58	235.027	11.447	
685	ATIC	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [source:swissprot;acc:p31939]	Subtracted	223.58	235.027	11.447	
685	HOXA5	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Divided	132.413	125.389	1.05602	
686		homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Divided	132.413	125.389	1.05602	
686	PAICS	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [source:swissprot;acc:p22234]	Subtracted	223.58	235.027	11.447	
687	EIF3M	dendritic cell protein. [source:refseq;acc:nm_006360]	Subtracted	223.121	211.685	11.436	
687	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Divided	132.413	125.389	1.05602	
688	CPXM2	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	Subtracted	223.121	211.685	11.436	
688	POLR2D	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	Divided	237.554	250.823	1.05586	
689	CPN1	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	Subtracted	223.121	211.685	11.436	
689	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Divided	135.379	128.225	1.05579	
690	CPZ	cpz gene product. [source:refseq;acc:nm_003652]	Subtracted	223.121	211.685	11.436	

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/