MK5 Microarray Data

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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 610 to 659 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
39	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Squared	Subtracted	1	226186	145568	80618
	ero1-like. [refseq;acc:nm_014584]	Ranked	Divided	0	13853	20536	1.48242
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Rooted	Subtracted	1	26.0288	43.1914	17.1626
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Measured	Divided		1836.8	907.903	2.02312
		Rooted			40.28	24.37	1.65285
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Ranked	Subtracted		268.565	334.483	65.918
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured			23693.7	18263	5430.7
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]		Divided	0	482.426	192.295	2.50878
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared		1	106226	192141	1.80879
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Rooted	Subtracted	0	30.9855	21.9983	8.9872
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Measured			973.698	1601.52	627.822
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted	Divided		7.90063	14.4058	1.82337
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Ranked		1	322	253	1.27273
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared	Subtracted	0	32743.7	27000	5743.7
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]		Divided		43.8625	5.33358	8.22384
40	60s ribosomal protein l21. [swissprot;acc:p46778]	Rooted	Subtracted		20.5734	29.2291	8.6557
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]		Divided		24.454	13.5647	1.80277
	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Squared	Subtracted	1	222655	143584	79071
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		Divided		144940	81169.7	1.78564
	deltex 2. [refseq;acc:nm_020892]	Ranked	Subtracted		333.144	267.393	65.751
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]		Divided		322	253	1.27273
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]			0	3845	5699	1.48218
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	Measured		1	1836.81	907.978	2.02297
		Rooted			40.2797	24.3705	1.65281
	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	Squared		0	5.83408	0.742249	7.86
	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]	Measured	Subtracted	1	23693.7	18263	5430.7
	nanos (fragment). [sptrembl;acc:q8wy41]		Divided	0	377	151	2.49669
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Ranked	Subtracted		7395	11625	4230
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Measured			148	773	625
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Rooted		1	26.0288	43.1914	17.1626
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Squared		0	105483	111123	5640
41	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Measured			6131.07	6739.34	608.27
	60s ribosomal protein l21. [swissprot;acc:p46778]	Ranked	Divided		9994.33	6758.83	1.47871
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]		Subtracted		7395	11625	4230
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]			1	332.925	267.274	65.651
	dystrophin. [swissprot;acc:p11532]	Squared	Divided	0	98.4011	12.5624	7.83299
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]		Subtracted		80280.6	74715.1	5565.5
	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]			1	214143	138337	75806
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Measured	Divided		1836.81	907.978	2.02297
		Rooted			40.2797	24.3705	1.65281
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Squared			144912	81155	1.78562
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Measured		0	266	645	2.42481
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Ranked		1	322	253	1.27273
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Rooted	Subtracted		60.8365	77.7233	16.8868
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]			0	42.8135	51.3517	8.5382
	suppressor of actin 1. [refseq;acc:nm_014016]		Divided		3.30572	5.87091	1.77599
	trophinin. [swissprot;acc:q12816]	Measured	Subtracted	1	23693.7	18263	5430.7
42	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	Divided	0	5.11118	9.0312	1.76695
	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Ranked			8158	5530.5	1.47509
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Squared	Subtracted	1	211446	137422	74024

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.