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 2401 to 2450 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
601	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	Squared	34129.6	40434.5	1.18473	
601	symplekin. [source:swissprot;acc:q92797]	Measured	15213.4	13418.1	1.1338	
601	vam6/vps39-like protein (hvam6p). [source:swissprot;acc:q96jc1]	Ranked	206.274	218.792	1.06069	
601	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Rooted	138.032	127.651	1.08132	
602	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	Measured	4864.66	5514.87	1.13366	
602	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Rooted	138.032	127.651	1.08132	
602	microtubule-associated protein 4 (map 4). [source:swissprot;acc:p27816]	Ranked	206.274	218.792	1.06069	
602	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Squared	19129.8	22652.9	1.18417	
603	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Measured	4864.66	5514.87	1.13366	
603	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	Ranked	225.829	212.945	1.0605	
603	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Squared	34071.5	40336.5	1.18388	
603	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	Rooted	60.0742	64.9418	1.08103	
604	60s ribosomal protein l15. [source:swissprot;acc:p39030]	Ranked	217.862	230.978	1.0602	
604	alpha-nac protein. [source:sptrembl;acc:q9h009]	Squared	34069.4	40333	1.18385	
604	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	Rooted	60.0742	64.9418	1.08103	
604	vinculin (metavinculin). [source:swissprot;acc:p18206]	Measured	5958.23	6743.37	1.13177	
605	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	Ranked	247.47	233.441	1.0601	
605	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Measured	6143.52	6950.75	1.1314	
605	sedlin. [source:swissprot;acc:o14582]	Rooted	116.061	125.434	1.08076	
605	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Squared	34068.1	40330.8	1.18383	
606	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [source:swissprot;acc:p98194]	Measured	6148.94	6955.76	1.13121	
606	di-ras2. [source:refseq;acc:nm_017594]	Squared	34068	40330.7	1.18383	
606	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Ranked	247.47	233.441	1.0601	
606	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Rooted	116.061	125.434	1.08076	
607	bet3 homolog. [source:swissprot;acc:o43617]	Rooted	116.061	125.434	1.08076	
607	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [source:swissprot;acc:q96kp4]	Squared	26583.8	31468.6	1.18375	
607	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Ranked	247.47	233.441	1.0601	
607	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	Measured	14976.4	13246.6	1.13058	
608	histone h2b. [source:refseq;acc:nm_175055]	Ranked	247.47	233.441	1.0601	
608	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [source:swissprot;acc:p22570]	Squared	24560.6	29071.1	1.18365	
608	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	Measured	4510.61	5098.74	1.13039	
608	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Rooted	59.6517	64.4642	1.08068	
609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Measured	3886.62	3438.82	1.13022	
609	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	Ranked	247.47	233.441	1.0601	
609	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	Rooted	62.9281	67.99	1.08044	
609	pyrroline 5-carboxylate reductase isoform. [source:refseq;acc:nm_013328]	Squared	12276.9	14526	1.1832	
610	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Rooted	136.706	126.565	1.08012	
610	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	Ranked	247.47	233.441	1.0601	
610	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	Measured	8430.03	9518.11	1.12907	
610	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Squared	12347.6	14594.8	1.18199	
611	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	Squared	23487.1	27726.3	1.18049	
611	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	Measured	5148.71	5811.74	1.12878	
611	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	Ranked	247.47	233.441	1.0601	
611	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Rooted	51.0091	55.0909	1.08002	
612	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	Measured	3975.77	4485.05	1.1281	
612	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	Rooted	57.1949	61.7633	1.07987	
612	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	Ranked	247.47	233.441	1.0601	
612	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Squared	18595.6	21936.3	1.17965	
613	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	Ranked	247.47	233.441	1.0601	
613	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	Rooted	57.1971	61.7626	1.07982	

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/