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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2182 to 2231 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
546	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	Rooted	66.082	71.6526	1.0843	
546	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Ranked	207.222	194.262	1.06671	
546	zinc finger protein t86. [source:swissprot;acc:o00488]	Measured	4052.77	4612.54	1.13812	
547	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	Rooted	66.082	71.6525	1.0843	
547	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Ranked	207.26	194.346	1.06645	
547	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [source:swissprot;acc:p31153]	Squared	25945.4	30892.3	1.19067	
547	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Measured	5291.92	6020.19	1.13762	
548	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Measured	8268.19	9405.85	1.13759	
548	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	Rooted	66.082	71.6525	1.0843	
548	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Ranked	207.26	194.346	1.06645	
548	vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [source:swissprot;acc:p19065]	Squared	27516.2	32720	1.18912	
549	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Measured	5865.79	6671.23	1.13731	
549	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	Rooted	66.082	71.6526	1.0843	
549	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Ranked	207.26	194.346	1.06645	
549	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [source:swissprot;acc:p23763]	Squared	27516.2	32720	1.18912	
550	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	Rooted	66.082	71.6525	1.0843	
550	prohibitin. [source:swissprot;acc:p35232]	Measured	5773.45	6563.69	1.13687	
550	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Ranked	207.26	194.346	1.06645	
550	vesicule-associated membrane protein 4 (vamp-4). [source:swissprot;acc:o75379]	Squared	27516.2	32720	1.18912	
551	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [source:swissprot;acc:o14735]	Squared	27516.2	32720	1.18912	
551	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	Rooted	66.082	71.6525	1.0843	
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]	Ranked	207.261	194.347	1.06645	
551	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	Measured	5773.45	6563.69	1.13687	
552	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [source:swissprot;acc:q8n6t3]	Squared	27516.2	32720	1.18912	
552	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	Measured	15427.2	13572.8	1.13663	
552	crk-like protein. [source:swissprot;acc:p46109]	Ranked	207.26	194.346	1.06645	
552	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	Rooted	66.082	71.6523	1.08429	
553	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Ranked	207.26	194.346	1.06645	
553	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	Rooted	66.082	71.6523	1.08429	
553	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Measured	3853.64	4379.71	1.13651	
553	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [source:swissprot;acc:q15836]	Squared	27516.2	32720	1.18912	
554	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	Rooted	66.0829	71.6462	1.08419	
554	pre-mrna cleavage complex ii protein clp1. [source:swissprot;acc:q92989]	Measured	14830.5	13050.3	1.13641	
554	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	Squared	8426.68	10010.8	1.18799	
554	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Ranked	207.26	194.346	1.06645	
555	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Ranked	207.26	194.346	1.06645	
555	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991]	Squared	8426.68	10010.8	1.18799	
555	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Measured	6167.93	7007.7	1.13615	
555	u4/u6-associated rna splicing factor. [source:refseq;acc:nm_004698]	Rooted	59.7823	64.7895	1.08376	
556	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Ranked	207.27	194.368	1.06638	
556	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	Squared	8426.68	10010.8	1.18799	
556	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Measured	6167.93	7007.7	1.13615	
556	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	Rooted	66.0911	71.6061	1.08345	
557	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Squared	8426.68	10010.8	1.18799	
557	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Ranked	207.272	194.371	1.06637	
557	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Measured	6167.93	7007.7	1.13615	
557	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Rooted	97.1967	105.302	1.08339	
558	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	Rooted	66.1583	71.6729	1.08335	
558	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Squared	8426.68	10010.8	1.18799	
558	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Measured	6167.93	7007.7	1.13615	

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/