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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1093 to 1142 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
547	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	Subtracted	234.106	248.104	13.998	
547	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Divided	207.26	194.346	1.06645	
548	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	
548	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Divided	207.26	194.346	1.06645	
549	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	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	
550	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	
550	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	
551	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	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	crk-like protein. [source:swissprot;acc:p46109]	Divided	207.26	194.346	1.06645	
552	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	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	
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	
554	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	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	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	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Divided	207.27	194.368	1.06638	
556	evolutionarily conserved g-patch domain containing. [source:refseq;acc:nm_018025]	Subtracted	227.86	213.945	13.915	
557	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Divided	207.272	194.371	1.06637	
557	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	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Divided	207.309	194.452	1.06612	
559	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	
560	son of sevenless protein homolog 1 (sos-1). [source:swissprot;acc:q07889]	Divided	205.74	193.021	1.06589	
560	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	Subtracted	232.118	218.406	13.712	
561	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	Divided	205.89	193.183	1.06578	
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	
562	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Subtracted	224.606	210.944	13.662	
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Divided	220.744	207.121	1.06577	
563	calcyphosine. [source:swissprot;acc:q13938]	Divided	220.744	207.121	1.06577	
563	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	Subtracted	224.606	210.944	13.662	
564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Divided	220.744	207.121	1.06577	
564	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Subtracted	220.744	207.121	13.623	
565	calcyphosine. [source:swissprot;acc:q13938]	Subtracted	220.744	207.121	13.623	
565	sedlin. [source:swissprot;acc:o14582]	Divided	129.219	121.261	1.06563	
566	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Subtracted	220.744	207.121	13.623	
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Divided	129.219	121.261	1.06563	
567	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	Subtracted	228.639	242.258	13.619	
567	bet3 homolog. [source:swissprot;acc:o43617]	Divided	129.219	121.261	1.06563	
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	Divided	226.3	212.38	1.06554	
568	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	Subtracted	228.639	242.258	13.619	
569	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	Subtracted	228.639	242.258	13.619	
569	t54 protein. [source:swissprot;acc:q92917]	Divided	226.3	212.38	1.06554	
570	sorting nexin 17. [source:swissprot;acc:q15036]	Subtracted	228.639	242.258	13.619	
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Divided	229.709	215.631	1.06529	
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	Divided	238.529	254.099	1.06528	
571	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	Subtracted	221.807	208.264	13.543	

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/