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 2180 to 2229 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
137	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Rooted	Subtracted	0	13.7191	17.6786	3.9595
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Ranked		1	263.191	231.394	31.797
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured		1	12786.6	10879.9	1906.7
	heat shock factor binding protein 1. [swissprot;acc:o75506]	Measured	Divided	0	1631.18	1233.41	1.3225
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Squared	Subtracted		26171.8	27038.8	867
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Ranked	Subtracted		16853	15123	1730
		Squared	Divided		0.417515	0.742249	1.77778
	musashi 2 isoform a. [refseq;acc:nm_138962]	Rooted		1	54.9787	66.2416	1.20486
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked		1	350	290	1.2069
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Measured	Subtracted	0	7520.78	7276.12	244.66
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Rooted	Divided	0	18.9056	15.8624	1.19185
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Squared	Subtracted	1	69549	92953.5	23404.5
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Rooted		1	49.2925	62.397	13.1045
138	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Measured		0	1663.73	1906.28	242.55
	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked		1	174.667	205.556	30.889
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Rooted		0	18.4959	14.5738	3.9221
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Squared		1	70739	93908.8	23169.8
	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	Rooted	Divided	0	22.775	19.1245	1.19088
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Squared	Subtracted	0	25552.2	26410.4	858.2
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Measured	Divided	1	2755.15	2094.3	1.31555
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Ranked		0	12384.7	10549.4	1.17397
	musashi 1. [refseq;acc:nm_002442]	Rooted		1	54.9787	66.2416	1.20486
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Squared			468498	322755	1.45156
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Ranked			194.372	234.204	1.20493
	serpin b11. [swissprot;acc:q96p15]	Ranked	Subtracted	0	16853	15123	1730
	serpin b11. [swissprot;acc:q96p15]	Squared	Divided	0	0.417515	0.742249	1.77778
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Measured	Subtracted	1	15182.5	13277.9	1904.6
	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	Measured	Divided	0	204.382	154.804	1.32026
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Rooted	Subtracted	1	49.293	62.3973	13.1043
139	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Rooted	Subtracted	0	5.11118	9.0312	3.92002
	alpha crystallin a chain. [swissprot;acc:p02489]	Ranked	Divided	0	16372.4	13972.2	1.17178
	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Ranked		1	271.752	225.68	1.20415
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Measured		0	736.737	561.038	1.31317
	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Measured	Subtracted	1	12780.7	10876.4	1904.3
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Ranked		1	287.41	256.835	30.575
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Ranked		0	16853	15123	1730
		Squared	Divided	0	0.417515	0.742249	1.77778
	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Squared		1	81592.1	56211.1	1.45153
	nuclear protein ukp68. [refseq;acc:nm_024824]	Rooted		1	54.9787	66.2416	1.20486
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Measured	Subtracted	0	3161.12	2924.8	236.32
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Measured	Divided	1	2759.61	2099.49	1.31442
	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	Squared	Subtracted	1	86861.5	65369.7	21491.8
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Squared		0	795.24	1645.86	850.62
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Rooted		1	49.3267	62.4167	13.09
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Rooted	Divided	0	19.6214	23.3024	1.1876
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Ranked	Subtracted	1	228.306	198.011	30.295
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Rooted	Divided	0	25.8457	21.7945	1.18588
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Squared	Divided	1	81527.6	56190.6	1.45091
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked	Subtracted	0	15081.8	16802.1	1720.3
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Rooted	Divided	1	55.6161	66.7332	1.19989

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/