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

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Showing element 2401 to 2450 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
301	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Ranked	1	150.982	166.372	1.10193
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Measured	1	13768.2	11466	1.20078
	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Rooted	0	12.7534	11.8854	1.07303
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Measured		135.294	149.371	1.10405
	kappa b-ras 1. [refseq;acc:nm_020345]	Squared		1558.15	1297.17	1.20119
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Rooted	1	203.673	182.638	1.11517
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Squared	1	28896.2	36767	1.27238
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Ranked	0	12783	13698	1.07158
302	60s ribosomal protein l26. [swissprot;acc:q02877]	Ranked	1	242.326	267.008	1.10185
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Squared	0	61.898	74.2593	1.1997
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Rooted	1	203.673	182.638	1.11517
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	Ranked	0	7386.71	6895.44	1.07125
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Measured		135.294	149.371	1.10405
	lats homolog 1. [refseq;acc:nm_004690]	Rooted		10.2412	9.54479	1.07296
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Measured	1	5894.75	7073.65	1.19999
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	Squared		28896.2	36767	1.27238
303	60s ribosomal protein l35. [swissprot;acc:p42766]	Ranked		242.333	266.999	1.10179
	crk-like protein. [swissprot;acc:p46109]	Squared		28896.2	36767	1.27238
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Rooted		203.673	182.638	1.11517
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Ranked	0	11431.4	12244.1	1.07109
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Squared	0	1487.24	1783.26	1.19904
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Measured	1	22268.8	18560.4	1.1998
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Measured	0	952.488	863.886	1.10256
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Rooted	0	10.2412	9.54479	1.07296
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Ranked	1	242.339	266.986	1.1017
	40s ribosomal protein s28. [swissprot;acc:p25112]	Squared	0	1054.58	879.603	1.19893
	cytohesin 4. [swissprot;acc:q9uia0]	Rooted	1	203.673	182.638	1.11517
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	Measured		4855.46	5824.52	1.19958
	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	Squared		28896.2	36767	1.27238
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Rooted	0	31.3568	29.2362	1.07253
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Ranked		8021.78	7496.8	1.07003
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Measured		4962.34	5469.68	1.10224
305	40s ribosomal protein s29. [swissprot;acc:p30054]	Squared		5295.67	6326.82	1.19472
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Rooted	1	203.673	182.638	1.11517
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Rooted	0	24.6278	26.4005	1.07198
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]	Ranked	0	9431	8815	1.06988
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Ranked	1	242.339	266.986	1.1017
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Measured		3856.29	4624.15	1.19912
	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	Squared		28896.2	36767	1.27238
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	Measured	0	4962.34	5469.68	1.10224
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Ranked	1	242.153	266.673	1.10126
	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Measured	0	1705.19	1547.2	1.10211
	pnas-18. [sptrembl;acc:q9bzu3]	Measured	1	13680.5	11409.6	1.19903
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Squared		28896.2	36767	1.27238
	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	Rooted		56.3935	62.8817	1.11505
	scribble. [refseq;acc:nm_015356]	Rooted	0	18.8966	17.6385	1.07133
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Squared		31.0895	37.1241	1.1941
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	Ranked		5540	5921	1.06877
307	60s ribosomal protein l7. [swissprot;acc:p18124]	Squared		5826.27	6955.21	1.19377
307	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Ranked		1091	1021	1.06856

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/