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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green

Results: HTML CSV LaTeX

Showing element 336 to 385 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	network_comparison	green
42	PBK	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Ranked	Subtracted	332.874	65.628	267.246
43	no value	jun dimerization protein. [refseq;acc:nm_130469]	Ranked	Divided	204.641	1.2714	160.957
	ATG3	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Measured	Subtracted	21785.2	5359.1	16426.1
	ATG4B	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Squared	Divided	144876	1.78558	81136.5
	FOSL2	fos-related antigen 2. [swissprot;acc:p15408]	Rooted	Subtracted	60.8675	16.8493	77.7168
	GNB1	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Rooted	Divided	40.6302	1.59677	25.4452
	GNB3	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Measured	Divided	1881.02	1.83093	1027.36
	KHDRBS3	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Ranked	Subtracted	332.874	65.628	267.246
	MYO5B	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Squared		110342	73956	184298
44	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Measured		28136.5	5321.1	33457.6
	FOSB	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Rooted		60.8692	16.8473	77.7165
	FOSL2	fos-related antigen 2. [swissprot;acc:p15408]	Ranked	Divided	204.641	1.2707	161.046
	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Squared		139741	1.78117	78454.6
	GNB1	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Measured		1931.34	1.82652	1057.39
	GNB4	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Rooted		40.5691	1.59556	25.4263
	KHDRBS1	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Ranked	Subtracted	332.874	65.628	267.246
	MYO5C	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Squared	Subtracted	110342	73956	184298
45	no value	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		Divided	129597	1.77148	73157.5
	no value	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]		Subtracted	110342	73956	184298
	FOSB	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Ranked	Divided	204.641	1.27066	161.051
	FOSL1	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Rooted	Subtracted	60.875	16.8402	77.7152
	GNB3	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Rooted	Divided	40.081	1.59339	25.1546
	GNB4	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Measured	Divided	1926.69	1.82448	1056.02
	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Ranked	Subtracted	332.874	65.628	267.246
	PPP1R7	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Measured	Subtracted	27642.5	5202.1	22440.4
46	ATG3	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Squared	Divided	129597	1.77148	73157.5
	CPSF4	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Measured	Subtracted	24896.4	4464.7	20431.7
	DTX2	deltex 2. [refseq;acc:nm_020892]	Rooted	Divided	27.634	1.5909	43.9629
	FOSL1	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Ranked	Divided	204.642	1.27053	161.068
	MAGED4	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted	Subtracted	137.446	16.623	120.823
	NEURL	neuralized-like. [refseq;acc:nm_004210]	Ranked	Subtracted	332.326	65.378	266.948
	NEUROD2	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Measured	Divided	779.167	1.78438	1390.33
	PAPOLA	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Squared	Subtracted	210445	73666	136779
47	no value	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	Divided	98517.9	1.73059	56927.2
	CHD3	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Measured		779.167	1.78438	1390.33
	DTX1	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Rooted		27.7078	1.58861	44.017
	EXOC2	exocyst complex component sec5. [swissprot;acc:q96kp1]	Squared	Subtracted	210335	73619	136716
	KIAA1012	trs85 homolog. [swissprot;acc:q9y2l5]	Measured		24896.4	4464.7	20431.7
	MAGEE2	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Rooted		137.446	16.623	120.823
	TMEM132A	gbp protein isoform a. [refseq;acc:nm_017870]	Ranked	Divided	325.586	1.26938	256.492
	TOB2	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Ranked	Subtracted	350	60	290
48	no value	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	Subtracted	137.446	16.623	120.823
	CDK2AP2	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Measured	Divided	779.167	1.78438	1390.33
	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Ranked		65.4586	1.26868	83.0461
	LASS2	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Squared		6300.2	1.69891	10703.5
	PAPOLG	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Squared	Subtracted	210199	73561	136638
	PBK	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Rooted	Divided	27.7254	1.58807	44.0299
	TOB1	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	Subtracted	350	60	290
	WDR33	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Measured	Subtracted	24806.9	4437	20369.9
49	ARRB2	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Ranked	Divided	133	1.26667	105

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
- Hugo is the HGNC identifier if it exists
- 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/