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 1075 to 1124 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
538	PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Subtracted	58	44	14	
538	POLR2L	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	Divided	237.627	253.604	1.06724	
539	MEMO1P	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	Divided	236.964	252.86	1.06708	
539	MYH2	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Subtracted	112	126	14	
540	PANK3	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Subtracted	58	44	14	
540	SEPHS2	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Divided	222.156	208.201	1.06703	
541	MICAL2	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Divided	222.156	208.201	1.06703	
541	MYH3	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Subtracted	112	126	14	
542	INPP4B	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Divided	222.156	208.201	1.06703	
542	MYH1	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Subtracted	112	126	14	
543		myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Subtracted	112	126	14	
543	SEPHS1	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Divided	222.156	208.201	1.06703	
544	INPP4A	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Divided	222.156	208.201	1.06703	
544	MYH7B	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Subtracted	112	126	14	
545	EIF6	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Divided	248.866	233.287	1.06678	
545	SLC25A43	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Subtracted	58	44	14	
546	MYH13	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Subtracted	112	126	14	
546	WAS	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Divided	207.222	194.262	1.06671	
547	AARS	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	Subtracted	234.106	248.104	13.998	
547	CRK	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Divided	207.26	194.346	1.06645	
548	ABL2	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Divided	207.26	194.346	1.06645	
548	SEPHS2	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Subtracted	222.156	208.201	13.955	
549		proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Divided	207.26	194.346	1.06645	
549	MICAL2	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Subtracted	222.156	208.201	13.955	
550	HCK	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Divided	207.26	194.346	1.06645	
550	INPP4B	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Subtracted	222.156	208.201	13.955	
551	GRAP2	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	Divided	207.261	194.347	1.06645	
551	SEPHS1	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Subtracted	222.156	208.201	13.955	
552	CRKL	crk-like protein. [source:swissprot;acc:p46109]	Divided	207.26	194.346	1.06645	
552	INPP4A	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Subtracted	222.156	208.201	13.955	
553		putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	Subtracted	226.3	212.38	13.92	
553	ABL1	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Divided	207.26	194.346	1.06645	
554	FYN	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Divided	207.26	194.346	1.06645	
554	GPKOW	t54 protein. [source:swissprot;acc:q92917]	Subtracted	226.3	212.38	13.92	
555		cbf1 interacting corepressor. [source:refseq;acc:nm_004882]	Subtracted	227.86	213.945	13.915	
555	FGR	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Divided	207.26	194.346	1.06645	
556	CUTL1	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Divided	207.27	194.368	1.06638	
556	GPATCH1	evolutionarily conserved g-patch domain containing. [source:refseq;acc:nm_018025]	Subtracted	227.86	213.945	13.915	
557	CUTL2	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Divided	207.272	194.371	1.06637	
557	SBDS	shwachman-bodian-diamond syndrome protein (cgi-97). [source:swissprot;acc:q9y3a5]	Subtracted	216.557	230.362	13.805	
558		tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Subtracted	248.994	235.255	13.739	
558		ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Divided	135.087	144.041	1.06628	
559	RPP30	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [source:swissprot;acc:p78346]	Subtracted	216.72	230.439	13.719	
559	WASL	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Divided	207.309	194.452	1.06612	
560	DR1	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	Subtracted	232.118	218.406	13.712	
560	SOS1	son of sevenless protein homolog 1 (sos-1). [source:swissprot;acc:q07889]	Divided	205.74	193.021	1.06589	
561		u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Subtracted	228.215	214.546	13.669	
561	SOS2	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	Divided	205.89	193.183	1.06578	
562	GULP1	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Divided	220.744	207.121	1.06577	
562	PRSS7	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Subtracted	224.606	210.944	13.662	

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/