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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Gene Rank description green Filtered Value Type Interaction Map Network Comparison Type red network_comparison

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Showing element 601 to 650 of 38536 in total

Network Comparison Type

: Divided

Rank	description	green	Filtered	Value Type	Interaction Map	red	network_comparison
38	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	35.5	0	Measured	Low confidence	105.5	2.97183
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	5.80679	0	Rooted	Low confidence	9.84765	1.69589
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	253	1	Ranked	High confidence	322	1.27273
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	192141		Squared	High confidence	106226	1.80879
	rab11-family interacting protein 4. [refseq;acc:nm_032932]	8696.7		Measured	Low confidence	7407.56	1.17403
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	6.97663	0	Rooted	High confidence	3.62029	1.92709
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	9243.55		Ranked	Low confidence	6768.72	1.36563
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	120.429		Measured	High confidence	320.012	2.65727
39	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]	8270.5		Ranked	Low confidence	11290	1.36509
	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	55.8176	1	Rooted		63.4164	1.13614
	eferin. [swissprot;acc:o75154]	8696.7	1	Measured		7407.56	1.17403
	ero1-like. [refseq;acc:nm_014584]	20536	0	Ranked	High confidence	13853	1.48242
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	282.937	1	Ranked	Low confidence	247.202	1.14456
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	24.37		Rooted	High confidence	40.28	1.65285
		907.903		Measured	High confidence	1836.8	2.02312
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	0.355148	0	Squared	Low confidence	3.41692	9.62112
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	35.5	0	Measured		105.5	2.97183
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	61881.5	1	Squared		82347.8	1.33073
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	5.80678	0	Rooted		9.84765	1.69589
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	192.295	0	Measured	High confidence	482.426	2.50878
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	192141	1	Squared		106226	1.80879
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	14.4058	0	Rooted		7.90063	1.82337
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	253	1	Ranked		322	1.27273
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	5.33358	0	Squared		43.8625	8.22384
40	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	13.5647	0	Rooted		24.454	1.80277
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	81169.7	1	Squared		144940	1.78564
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	253	1	Ranked		322	1.27273
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	5699	0	Ranked		3845	1.48218
	fos-related antigen 2. [swissprot;acc:p15408]	7600.25	1	Measured	Low confidence	6480.59	1.17277
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	15924	0	Ranked	Low confidence	11761	1.35397
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	24.3705	1	Rooted	High confidence	40.2797	1.65281
		907.978	1	Measured		1836.81	2.02297
	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	0.742249	0	Squared		5.83408	7.86
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	35.5		Measured	Low confidence	105.5	2.97183
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	5.80678		Rooted		9.84765	1.69589
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	61881.5	1	Squared		82347.8	1.33073
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	0.355148	0	Squared		3.41692	9.62112
	nanos (fragment). [sptrembl;acc:q8wy41]	151	0	Measured	High confidence	377	2.49669
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	63.2842	1	Rooted	Low confidence	55.7075	1.13601
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	223.538	1	Ranked	Low confidence	255.382	1.14245
41	60s ribosomal protein l21. [swissprot;acc:p46778]	6758.83	0		High confidence	9994.33	1.47871
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	200.55	1		Low confidence	228.147	1.13761
	dystrophin. [swissprot;acc:p11532]	12.5624	0	Squared	High confidence	98.4011	7.83299
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	24.3705	1	Rooted		40.2797	1.65281
		907.978	1	Measured		1836.81	2.02297
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	35.5	0	Measured	Low confidence	105.5	2.97183
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	61881.5	1	Squared		82347.8	1.33073
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	5.80678	0	Rooted		9.84765	1.69589
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	0.355148	0	Squared		3.41692	9.62112
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	63.2842	1	Rooted		55.7075	1.13601

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/