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.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 551 to 600 of 77072 in total

Rank	description	Network Comparison Type	Interaction Map	Filtered	Value Type	red	network_comparison	green
18	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	Divided	Low confidence	0	Squared	2.31976	27.1495	0.0854438
		Divided	Low confidence		Rooted	9.94987	2.28266	4.3589
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Subtracted	High confidence		Squared	43393.5	13265.1	56658.6
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Divided	Low confidence	1	Measured	5492.04	1.32027	7251
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Subtracted	High confidence		Rooted	203.673	21.035	182.638
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Divided	High confidence		Rooted	21.4476	1.72261	36.9459
	early hematopoietic zinc finger. [refseq;acc:nm_015461]	Divided	Low confidence	0	Ranked	5850.23	1.52187	8903.28
	elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9]	Subtracted	Low confidence			16116.4	4611.4	11505
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]		High confidence			7509.39	6668.71	14178.1
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		High confidence	1		266.865	69.316	336.181
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]		Low confidence	1	Measured	15464.1	2108.6	17572.7
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	High confidence	0	Ranked	22286	1.68629	13216
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	Low confidence	0	Rooted	0	9.43398	9.43398
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Subtracted		1	Squared	122475	37292	159767
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Divided			Ranked	305.303	1.2352	247.169
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Subtracted	High confidence		Squared	219048	89286	129762
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]		High confidence		Measured	24255.7	6086.8	18168.9
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Low confidence	0	Measured	859	801	58
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided		1	Squared	332411	1.42416	473408
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Divided			Rooted	44.4168	1.25937	55.937
		Subtracted			Ranked	273.188	40.698	232.49
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Divided	High confidence		Measured	677.5	2.75351	1865.5
		Divided			Squared	108.641	7.58176	823.69
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Subtracted		0	Rooted	12.4097	12.4097	0
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]		Low confidence	1	Rooted	32.2231	15.7049	47.928
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]		Low confidence	0	Squared	9955.21	8769.19	18724.4
19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Divided	High confidence	0	Measured	305.45	11.6763	26.1599
		Divided	Low confidence	1	Measured	3032.56	1.29112	3915.4
	alpha 2 globin. [refseq;acc:nm_000517]	Subtracted	Low confidence	0	Ranked	11486.2	4500.9	15987.1
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		High confidence	1	Measured	24250	6085.1	18164.9
	cytohesin 4. [swissprot;acc:q9uia0]			1	Rooted	203.673	21.035	182.638
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]			0	Measured	1593	1211	2804
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Divided	Low confidence			153	4.3268	662
	fos-related antigen 2. [swissprot;acc:p15408]	Subtracted	Low confidence			3205.98	798.71	2407.27
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Divided	High confidence	1	Ranked	185.678	1.32082	245.247
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Subtracted	High confidence			266.865	69.313	336.178
	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]		Low confidence			188.298	40.211	228.509
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]			0	Rooted	0	9.43398	9.43398
				1	Measured	15464.1	2108.6	17572.7
	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]			1	Squared	122475	37292	159767
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	High confidence	0	Ranked	22286	1.68629	13216
	l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338]		Low confidence		Rooted	3.94084	2.15887	8.50775
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		High confidence		Rooted	9.20014	6.52932	60.0707
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Subtracted		1	Squared	219048	89286	129762
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Divided			Measured	677.5	2.75351	1865.5
		Divided			Squared	108.641	7.58176	823.69
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Subtracted		0	Ranked	4475.84	6608.06	11083.9
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	Low confidence		Ranked	3208.8	1.5182	4871.6
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	High confidence		Squared	10489.8	12936.7	23426.5
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Subtracted	High confidence		Rooted	23.8747	12.0849	11.7898

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/