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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2613 to 2662 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2613	ARL1	adp-ribosylation factor-like protein 1. [source:swissprot;acc:p40616]	215.497	215.799	1.0014	
2614	RELA	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [source:swissprot;acc:q04206]	202.821	202.54	1.00139	
2615	RELB	transcription factor relb (i-rel). [source:swissprot;acc:q01201]	202.821	202.54	1.00139	
2616	NFKBIA	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [source:swissprot;acc:p25963]	202.821	202.54	1.00139	
2617	CPOX	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [source:swissprot;acc:p36551]	202.821	202.54	1.00139	
2618	IDH2	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [source:swissprot;acc:p48735]	190.166	190.429	1.00138	
2619	SMARCC2	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	220.024	219.722	1.00137	
2620	PSMD9	26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [source:swissprot;acc:o00233]	215.615	215.91	1.00137	
2621		dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [source:sptrembl;acc:q9h5b6]	224.891	225.195	1.00135	
2622	ZMYM6	zinc finger protein 258. [source:refseq;acc:nm_145310]	224.891	225.195	1.00135	
2623	ZMYM3	zinc finger protein 261 (dxs6673e protein). [source:swissprot;acc:q14202]	224.891	225.195	1.00135	
2624	ZMYM4	zinc finger protein 262; cell death inhibiting rna. [source:refseq;acc:nm_005095]	224.891	225.195	1.00135	
2625	WTAP	wilms' tumor 1-associating protein (wt1-associated protein). [source:swissprot;acc:q15007]	204.304	204.028	1.00135	
2626	ACTR2	actin-like protein 2 (actin-related protein 2). [source:swissprot;acc:o15142]	224.891	225.195	1.00135	
2627	COG3	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [source:swissprot;acc:q96jb2]	224.891	225.195	1.00135	
2628	ACTR3B	similar to actin-related protein 3-beta. [source:sptrembl;acc:q96bt2]	224.891	225.195	1.00135	
2629	ARPC1B	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [source:swissprot;acc:o15143]	224.891	225.195	1.00135	
2630	ZMYM2	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [source:swissprot;acc:q9ubw7]	224.891	225.195	1.00135	
2631	ACTR3	actin-like protein 3 (actin-related protein 3) (actin-2). [source:swissprot;acc:p32391]	224.891	225.195	1.00135	
2632	ARPC3	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [source:swissprot;acc:o15145]	224.891	225.195	1.00135	
2633	NRD1	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [source:swissprot;acc:o43847]	224.891	225.195	1.00135	
2634	ARPC1A	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [source:swissprot;acc:q92747]	224.891	225.195	1.00135	
2635	CLP1	pre-mrna cleavage complex ii protein clp1. [source:swissprot;acc:q92989]	166.612	166.393	1.00132	
2636	ANAPC11	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	195.635	195.384	1.00128	
2637		small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	187.075	186.84	1.00126	
2638	F11R	junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [source:swissprot;acc:q9y624]	204.911	205.168	1.00125	
2639	MYO7A	myosin viia. [source:swissprot;acc:q13402]	220.658	220.386	1.00123	
2640	UBE2B	ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [source:swissprot;acc:p23567]	220.658	220.386	1.00123	
2641	UBE2A	ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [source:swissprot;acc:p49459]	220.658	220.386	1.00123	
2642	TOPBP1	topoisomerase (dna) ii binding protein. [source:refseq;acc:nm_007027]	194.097	194.328	1.00119	
2643	ACOX1	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [source:swissprot;acc:q15067]	194.097	194.328	1.00119	
2644	ATP5J2	atp synthase f chain, mitochondrial (ec 3.6.3.14). [source:swissprot;acc:p56134]	194.097	194.328	1.00119	
2645	DHX35	probable atp-dependent helicase ddx35 (deah-box protein 35). [source:swissprot;acc:q9h5z1]	194.097	194.328	1.00119	
2646	TSC22D4	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [source:swissprot;acc:q9y3q8]	213.169	213.417	1.00116	
2647	MAT1A	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [source:swissprot;acc:q00266]	212.496	212.25	1.00116	
2648	DEGS1	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [source:refseq;acc:nm_003676]	213.169	213.417	1.00116	
2649		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	213.63	213.874	1.00114	
2650	KHSRP	kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [source:refseq;acc:nm_003685]	217.188	216.942	1.00113	
2651	NFKBIE	nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [source:swissprot;acc:o00221]	201.37	201.594	1.00111	
2652	NFKB1	nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [source:swissprot;acc:p19838]	201.451	201.673	1.0011	
2653	NFKBIB	nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [source:swissprot;acc:q15653]	201.452	201.674	1.0011	
2654	NFKB2	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [source:swissprot;acc:q00653]	201.452	201.674	1.0011	
2655	BCL3	b-cell lymphoma 3-encoded protein (bcl-3 protein). [source:swissprot;acc:p20749]	201.445	201.667	1.0011	
2656	FUBP1	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [source:refseq;acc:nm_003902]	217.179	216.943	1.00109	
2657	DLG2	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [source:swissprot;acc:q15700]	216.934	216.7	1.00108	
2658	DLG4	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [source:swissprot;acc:p78352]	216.933	216.7	1.00108	
2659	DLG3	presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [source:swissprot;acc:q92796]	216.933	216.7	1.00108	
2660	DLG1	presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [source:swissprot;acc:q12959]	216.937	216.704	1.00108	
2661	FES	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [source:swissprot;acc:p07332]	204.768	204.549	1.00107	
2662	MOCS2	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [source:swissprot;acc:o96007]	204.768	204.549	1.00107	

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/