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 2508 to 2557 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2508	CEECAM1	cerebral cell adhesion molecule. [source:refseq;acc:nm_016174]	194.349	193.871	1.00247	
2509	CBX3	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [source:swissprot;acc:q13185]	187.902	188.366	1.00247	
2510	GRPEL2	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [source:swissprot;acc:q8taa5]	234.384	234.948	1.00241	
2511	GRPEL1	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [source:swissprot;acc:q9hav7]	234.384	234.948	1.00241	
2512	SMARCD2	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [source:refseq;acc:nm_003077]	234.384	234.948	1.00241	
2513	SMARCD3	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [source:refseq;acc:nm_003078]	234.384	234.948	1.00241	
2514	SMARCD1	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	234.384	234.948	1.00241	
2515	DFFB	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [source:swissprot;acc:o76075]	215.835	216.341	1.00234	
2516	ADAMTS9	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [source:swissprot;acc:q9p2n4]	215.835	216.341	1.00234	
2517	DFFA	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [source:swissprot;acc:o00273]	215.835	216.341	1.00234	
2518	ANK3	ankyrin 3 (ank-3) (ankyrin g). [source:swissprot;acc:q12955]	215.835	216.341	1.00234	
2519	ANK2	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [source:swissprot;acc:q01484]	215.835	216.341	1.00234	
2520	ARL3	adp-ribosylation factor-like protein 3. [source:swissprot;acc:p36405]	215.835	216.341	1.00234	
2521		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	201.96	201.488	1.00234	
2522	UNC119	unc-119 protein homolog (retinal protein 4) (hrg4). [source:swissprot;acc:q13432]	215.835	216.341	1.00234	
2523	KPNB1	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [source:swissprot;acc:q14974]	201.96	201.488	1.00234	
2524	TBL1X	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	201.96	201.488	1.00234	
2525	PSMD8	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [source:swissprot;acc:p48556]	215.835	216.341	1.00234	
2526	TBL1Y	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	201.96	201.488	1.00234	
2527	TKTL1	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	209.143	208.659	1.00232	
2528	SCRIB	scribble. [source:refseq;acc:nm_015356]	221.782	222.291	1.0023	
2529	LRRC1	lap (leucine-rich repeats and pdz) and no pdz protein. [source:refseq;acc:nm_018214]	221.776	222.283	1.00229	
2530		proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [source:swissprot;acc:p28062]	212.464	211.99	1.00224	
2531	APEX2	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [source:refseq;acc:nm_014481]	216.264	215.787	1.00221	
2532	NONO	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	190.405	190.812	1.00214	
2533	PSPC1	paraspeckle protein 1. [source:refseq;acc:nm_018282]	190.417	190.824	1.00214	
2534	GPD2	glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [source:swissprot;acc:p43304]	208	207.555	1.00214	
2535	CBX1	chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [source:swissprot;acc:p23197]	188.228	188.63	1.00214	
2536	GGPS1	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [source:swissprot;acc:o95749]	236.51	236.008	1.00213	
2537	VPS45	vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [source:swissprot;acc:q9nrw7]	215.964	216.421	1.00212	
2538	SFPQ	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [source:swissprot;acc:p23246]	190.765	191.163	1.00209	
2539	C21orf66	gc-rich sequence dna-binding factor homolog. [source:swissprot;acc:q9y5b6]	217.144	216.699	1.00205	
2540	TLR2	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [source:swissprot;acc:o60603]	217.144	216.699	1.00205	
2541	DARS	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [source:swissprot;acc:p14868]	194.505	194.902	1.00204	
2542	ING4	p29ing4; candidate tumor suppressor p33 ing1 homolog. [source:refseq;acc:nm_016162]	218.068	217.633	1.002	
2543	BRPF1	tubulin tyrosine ligase-like protein hottl (hqp0207). [source:swissprot;acc:q9y4r7]	224.726	225.164	1.00195	
2544	AMT	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [source:swissprot;acc:p48728]	212.67	212.262	1.00192	
2545		proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [source:swissprot;acc:p28065]	213.494	213.088	1.00191	
2546	TAF9B	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [source:refseq;acc:nm_015975]	197.138	197.507	1.00187	
2547		glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14410]	206.894	206.51	1.00186	
2548		glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14409]	206.899	206.516	1.00185	
2549		glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:p32189]	206.902	206.519	1.00185	
2550	EPN2	epsin 2 isoform b; eps15 binding protein. [source:refseq;acc:nm_014964]	217.587	217.988	1.00184	
2551	FBP2	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	209.766	210.148	1.00182	
2552	CDY1B	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	193.12	193.467	1.0018	
2553	CDYL	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [source:refseq;acc:nm_004824]	193.12	193.467	1.0018	
2554	CDY2B	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	193.12	193.467	1.0018	
2555	MAT2A	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [source:swissprot;acc:p31153]	212.953	212.572	1.00179	
2556	CDYL2	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	193.119	193.46	1.00177	
2557	EEF2	elongation factor 2 (ef-2). [source:swissprot;acc:p13639]	222.658	223.047	1.00175	

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/