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 1608 to 1657 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
402	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	Ranked	207.908	226.218	1.08807	
403	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Measured	5201.41	4479.76	1.16109	
403	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Squared	39463.9	48362.1	1.22548	
403	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Rooted	59.6834	65.6741	1.10037	
403	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	Ranked	207.908	226.218	1.08807	
404	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source:swissprot;acc:p30520]	Squared	26819.1	32855.4	1.22507	
404	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	Ranked	207.908	226.218	1.08807	
404	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Measured	5201.41	4479.76	1.16109	
404	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Rooted	59.6834	65.6741	1.10037	
405	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	Squared	26822.2	32858.1	1.22503	
405	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Rooted	116.576	105.948	1.10031	
405	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	Ranked	207.931	226.209	1.0879	
405	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Measured	5201.41	4479.76	1.16109	
406	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Rooted	49.9858	45.4433	1.09996	
406	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	Squared	18995.7	23245.6	1.22373	
406	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Measured	5201.41	4479.76	1.16109	
406	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	Ranked	265.634	244.304	1.08731	
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	Ranked	239.75	260.544	1.08673	
407	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Rooted	49.9856	45.4431	1.09996	
407	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Squared	18995.7	23244.9	1.22369	
407	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Measured	6603.41	7664.65	1.16071	
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	Ranked	255.112	234.804	1.08649	
408	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	Rooted	49.9856	45.4432	1.09996	
408	dok-like protein. [source:refseq;acc:nm_024872]	Measured	6102.59	7081.46	1.1604	
408	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	Squared	18995.7	23244.7	1.22368	
409	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Measured	6102.59	7081.46	1.1604	
409	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	Rooted	50.4409	45.8795	1.09942	
409	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	Ranked	241.045	261.874	1.08641	
409	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Squared	18995.6	23242.8	1.22359	
410	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Squared	19546.1	23881.6	1.22181	
410	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Measured	6102.59	7081.46	1.1604	
410	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	Rooted	55.5489	50.535	1.09922	
410	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	Ranked	233.376	253.539	1.0864	
411	pp3111 protein. [source:refseq;acc:nm_022156]	Rooted	55.5489	50.535	1.09922	
411	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Squared	17861.2	21821.8	1.22174	
411	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [source:swissprot;acc:p32780]	Ranked	233.376	253.539	1.0864	
411	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Measured	6102.59	7081.46	1.1604	
412	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	Measured	3594.31	4169.95	1.16015	
412	syntaxin 18. [source:swissprot;acc:q9p2w9]	Rooted	55.5489	50.535	1.09922	
412	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Squared	19556	23891.8	1.22171	
412	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	Ranked	240.788	261.416	1.08567	
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	Ranked	240.913	261.45	1.08525	
413	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]	Squared	19568.3	23904.6	1.2216	
413	rd protein. [source:swissprot;acc:p18615]	Rooted	55.5489	50.535	1.09922	
413	vav proto-oncogene. [source:swissprot;acc:p15498]	Measured	6644.99	7707.8	1.15994	
414	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	Measured	6744.05	5815.13	1.15974	
414	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]	Squared	22109.6	26989.4	1.22071	
414	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	Rooted	55.5489	50.535	1.09922	
414	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	Ranked	232.431	252.238	1.08522	
415	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	Rooted	55.5489	50.535	1.09922	

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/