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 2625 to 2674 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
329	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Rooted	Divided	50.3803	45.4193	1.10923	
329	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	Measured	Subtracted	11773	10733.2	1039.8	
329	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Ranked	Subtracted	191.644	170.192	21.452	
329	metaxin 2. [source:swissprot;acc:o75431]	Squared	Divided	41236	51807	1.25635	
329	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Squared	Subtracted	19321	12542.6	6778.4	
329	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Ranked	Divided	312	284	1.09859	
329	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Measured	Divided	15999.1	19007.1	1.18801	
329	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Rooted	Subtracted	124.41	117.043	7.367	
330	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Rooted	Divided	50.519	45.5497	1.1091	
330	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Ranked	Divided	312	284	1.09859	
330	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Ranked	Subtracted	224.657	203.235	21.422	
330	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	Measured	Subtracted	11773	10733.2	1039.8	
330	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Squared	Divided	16203.4	20339.9	1.25529	
330	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Squared	Subtracted	19321	12542.6	6778.4	
330	septin 6. [source:swissprot;acc:q14141]	Measured	Divided	15959.9	18957.1	1.1878	
330	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Rooted	Subtracted	55.5965	62.9349	7.3384	
331	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Rooted	Divided	60.6697	67.2802	1.10896	
331	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Ranked	Divided	312	284	1.09859	
331	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	Measured	Subtracted	10246.1	11285.8	1039.7	
331	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Squared	Subtracted	19321	12542.6	6778.4	
331	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Rooted	Subtracted	55.5965	62.9349	7.3384	
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Measured	Divided	20287.2	17083.8	1.18751	
331	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Squared	Divided	33100.3	41520.6	1.25439	
331	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Ranked	Subtracted	224.647	203.242	21.405	
332	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Squared	Subtracted	19321	12542.6	6778.4	
332	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Ranked	Subtracted	224.633	203.251	21.382	
332	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Rooted	Subtracted	59.0951	66.4332	7.3381	
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Ranked	Divided	312	284	1.09859	
332	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Squared	Divided	14464.3	18142.8	1.25432	
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Measured	Divided	5051.16	5975.51	1.183	
332	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Rooted	Divided	60.6732	67.2827	1.10894	
332	vav-2 protein. [source:swissprot;acc:p52735]	Measured	Subtracted	6660.02	7697.78	1037.76	
333	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Rooted	Subtracted	95.4476	102.785	7.3374	
333	deltex 2. [source:refseq;acc:nm_020892]	Measured	Subtracted	1618.84	2651.88	1033.04	
333	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Squared	Subtracted	19321	12542.6	6778.4	
333	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Ranked	Divided	312	284	1.09859	
333	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Measured	Divided	5039.63	5961.83	1.18299	
333	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	Rooted	Divided	49.0526	54.3781	1.10857	
333	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Squared	Divided	14464.3	18142.8	1.25432	
333	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	Ranked	Subtracted	265.634	244.304	21.33	
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	Squared	Divided	64975.9	81151.2	1.24894	
334	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Measured	Subtracted	1629.21	2662.12	1032.91	
334	e-1 enzyme. [source:refseq;acc:nm_021204]	Squared	Subtracted	30903.8	37638.1	6734.3	
334	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Ranked	Divided	312	284	1.09859	
334	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Rooted	Divided	58.6096	64.9655	1.10844	
334	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Ranked	Subtracted	232.473	211.207	21.266	
334	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Measured	Divided	14924.4	17655.2	1.18298	
334	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Rooted	Subtracted	58.2964	65.5926	7.2962	
335	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Rooted	Divided	50.4705	45.5342	1.10841	
335	60s ribosomal protein l24 (l30). [source:swissprot;acc:p38663]	Squared	Subtracted	30924.3	37652.3	6728	

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/