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 3258 to 3307 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
204	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Measured	Divided	1	4512.19	5655.52	1.25339
		Rooted			55.8956	63.9636	1.14434
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Squared			12326.4	16522.9	1.34045
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]		Subtracted		42411.6	55802.1	13390.5
	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]			0	18485.5	18144.8	340.7
		Rooted			32.8937	30.117	2.7767
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Measured	Divided		7981.68	6685.11	1.19395
205	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Measured	Subtracted		1183.16	1337.54	154.38
		Ranked	Subtracted		12183	11013.2	1169.8
	60s ribosomal protein l23a. [swissprot;acc:p29316]		Divided		11844.9	10636.3	1.11363
	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]		Subtracted	1	268.635	243.592	25.043
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Rooted	Subtracted	0	33.1655	30.4161	2.7494
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Ranked	Divided	1	228.1	200.968	1.13501
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Squared	Divided		12326.4	16522.9	1.34045
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Rooted	Subtracted		114.309	124.527	10.218
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Measured	Divided		4512.19	5655.52	1.25339
		Rooted			55.8956	63.9636	1.14434
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Measured		0	5418.2	4543.75	1.19245
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Rooted		0	23.8722	20.9337	1.14037
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Squared	Subtracted	1	40982.6	54272.3	13289.7
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]		Divided	0	99.0201	139.876	1.4126
	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]		Subtracted	0	18489.4	18148.7	340.7
	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Measured		1	10603.5	12069.4	1465.9
206	40s ribosomal protein s15a. [swissprot;acc:p39027]	Ranked		1	241.411	266.414	25.003
	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Rooted		0	74.2677	71.5378	2.7299
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Measured	Divided	1	5720.25	4577.5	1.24965
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Squared		1	12326.4	16522.9	1.34045
	espin. [refseq;acc:nm_031475]	Rooted		0	23.8722	20.934	1.14036
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Rooted		1	140.508	122.878	1.14348
	gk001 protein. [refseq;acc:nm_020198]	Measured	Subtracted	1	10603.5	12069.4	1465.9
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Ranked	Divided	0	7479	6716	1.11361
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Ranked	Divided	1	228.085	201.006	1.13472
	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	Squared	Subtracted	1	46739.9	59134.5	12394.6
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Measured		0	154	0	154
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Rooted		1	45.4558	55.5995	10.1437
	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]	Squared		0	18105.2	17795.2	310
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Measured	Divided		1124.15	943.423	1.19157
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Ranked	Subtracted		10634.4	9465	1169.4
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Squared	Divided		8.27667	5.86733	1.41064
207	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Rooted		1	140.508	122.878	1.14348
	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Squared		0	73080.8	102814	1.40685
	calcyphosine. [swissprot;acc:q13938]	Rooted	Subtracted	0	18.8902	21.6141	2.7239
	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	Measured	Subtracted	1	10600.3	12065.2	1464.9
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Measured	Divided	0	403.827	339.154	1.19069
	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Rooted	Subtracted	1	136.706	126.565	10.141
	dc11 protein. [refseq;acc:nm_020186]	Ranked	Divided	0	7479	6716	1.11361
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Ranked	Subtracted	1	237.312	212.363	24.949
	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	Squared		0	1775.39	1465.73	309.66
	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	Squared		1	46739.9	59134.5	12394.6
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Ranked	Divided	1	285.684	252.234	1.13261

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/