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 1114 to 1163 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
140	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Squared	1	81527.6	56190.6	1.45091
	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		55.6161	66.7332	1.19989
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Measured		2760.28	2100.27	1.31425
	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]	Ranked	0	16411.9	14027.1	1.17001
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	Squared	0	677.989	382.311	1.7734
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Ranked	1	59	49	1.20408
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Measured	0	934.726	1222.89	1.30829
141	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Squared		15.0305	26.5621	1.76721
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Measured		1161.88	891.114	1.30385
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Squared	1	81520.8	56188.5	1.45084
	lamin b2. [swissprot;acc:q03252]	Rooted	0	17.4452	14.7595	1.18196
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Ranked	0	7690.02	8991.19	1.1692
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Ranked	1	59	49	1.20408
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Rooted		55.6161	66.7332	1.19989
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Measured		4405.4	5782.08	1.3125
142	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Rooted	0	21.0926	17.849	1.18172
	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Squared	1	81478.9	56175.2	1.45044
	heat shock factor binding protein 1. [swissprot;acc:o75506]	Squared	0	3647.42	2072.05	1.7603
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Measured	1	9276.47	7090.37	1.30832
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Measured	0	874	1139	1.3032
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Rooted	1	55.6161	66.7332	1.19989
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Ranked	1	59	49	1.20408
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]		0	8214.41	7026.41	1.16908
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]		1	59	49	1.20408
	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Measured	1	9275.1	7089.65	1.30826
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Ranked	0	11124.8	13005.3	1.16904
	importin 4. [refseq;acc:nm_024658]	Rooted	0	16.4019	13.9084	1.17928
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Rooted	1	55.6161	66.7332	1.19989
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Squared	1	124319	86848.2	1.43145
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Measured	0	187	144	1.29861
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Squared		634.375	361.911	1.75285
144	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Ranked		11123.4	13000.1	1.16872
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Ranked	1	265.686	319.651	1.20312
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Squared	0	207.597	118.463	1.75242
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Measured	1	3349.9	4362.61	1.30231
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Squared		123324	86277.9	1.42938
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Rooted		55.6161	66.7332	1.19989
	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]	Rooted	0	9.72761	8.25872	1.17786
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Measured		633.433	821.711	1.29723
145	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Squared		255.854	146.067	1.75162
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Rooted	1	55.6161	66.7332	1.19989
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Measured	0	287.903	372.961	1.29544
	methyltransferase like 2. [refseq;acc:nm_018396]	Rooted	0	5.56776	6.55744	1.17775
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	1	310840	442993	1.42515
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Ranked	1	265.639	319.546	1.20293
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Ranked	0	7955.61	6817.49	1.16694
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	1	16771.5	12889.1	1.30122
146	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Measured	1	11068	8508.5	1.30082
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Ranked	0	12577.8	14662.1	1.16571
	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	Measured	0	291.639	377.574	1.29466

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/