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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 60274 to 60323 of 66312 in total

Network Comparison Type  : Subtracted
Interaction Map  : Low confidence
Filtered  : 1

Rank	Value Type	description	Hugo	network_comparison	red	green
3552	Ranked	fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]	AKTIP	2.909	203.212	200.303
	Squared	60s ribosomal protein l30. [swissprot;acc:p04645]	RPL30	1378.9	43077.8	41698.9
	Rooted	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	no value	2.1647	73.0501	75.2148
3553	Measured	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	PEX19	203.37	7951.73	8155.1
	Ranked	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	no value	2.906	199.463	196.557
	Squared	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153]	PAK1	1378.9	45514.3	44135.4
	Rooted	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	TCP1	2.1644	72.9622	75.1266
3554	Measured	80 kda nuclear cap binding protein (ncbp 80 kda subunit) (cbp80). [swissprot;acc:q09161]	NCBP1	203.37	7951.73	8155.1
	Ranked	spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020]	SPTBN2	2.901	197.276	194.375
	Squared	rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	RAB3IL1	1378.7	45696.4	44317.7
	Rooted	signal recognition particle 72 kda protein (srp72). [swissprot;acc:o76094]	SRP72	2.1638	74.1991	76.3629
3555	Measured	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	EXOSC10	203.35	7881.04	8084.39
	Ranked	cytosolic ovarian carcinoma antigen 1 (apk1 antigen). [swissprot;acc:q16206]	ENOX2	2.901	203.012	200.111
	Squared	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	no value	1378.4	46112.5	44734.1
	Rooted	nude nuclear distribution gene e homolog like 1 (a. nidulans); lis1-interacting protein nudel; endooligopeptidase a. [refseq;acc:nm_030808]	NDEL1	2.1626	73.4315	75.5941
3556	Measured	guanine nucleotide-binding protein g(s), alpha subunit (adenylate cyclase-stimulating g alpha protein). [swissprot;acc:p04895]	GNAS	203.28	8081.28	8284.56
	Ranked	spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082]	SPTBN1	2.901	197.276	194.375
	Squared	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	TAF5	1378.3	44351.7	42973.4
	Rooted	ubiquitin protein ligase. [refseq;acc:nm_130466]	UBE3B	2.1624	73.7104	75.8728
3557	Measured	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	no value	203.2	7669.39	7872.59
	Ranked	sodium/potassium-transporting atpase beta-1 chain (sodium/potassium- dependent atpase beta-1 subunit). [swissprot;acc:p05026]	ATP1B1	2.899	196.98	194.081
	Squared	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	no value	1378.2	47708.6	46330.4
	Rooted	mitochondrial ribosomal protein s7; 30s ribosomal protein s7 homolog. [refseq;acc:nm_015971]	MRPS7	2.1624	73.7104	75.8728
3558	Measured	guanine nucleotide-binding protein g(olf), alpha subunit (adenylate cyclase-stimulating g alpha protein, olfactory type). [swissprot;acc:p38405]	GNAL	203.18	8081.23	8284.41
	Ranked	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]	C3orf60	2.897	204.488	201.591
	Squared	excision repair protein ercc-6 (cockayne syndrome protein csb). [swissprot;acc:q03468]	PGBD3	1377.7	43224.6	41846.9
	Rooted	scribble. [refseq;acc:nm_015356]	SCRIB	2.1623	71.654	73.8163
3559	Measured	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	DLG2	203.11	7939.05	8142.16
	Ranked	ras-related protein rab-5a. [swissprot;acc:p20339]	RAB5A	2.896	199.052	196.156
	Squared	diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907]	DGAT1	1377.4	45556.3	46933.7
	Rooted	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	PEX1	2.1621	72.2261	74.3882
3560	Measured	protein farnesyltransferase beta subunit (ec 2.5.1.-) (caax farnesyltransferase beta subunit) (ras proteins prenyltransferase beta) (ftase-beta). [swissprot;acc:p49356]	FNTB	203.03	7931.27	8134.3
	Ranked	sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280]	ODF3	2.895	201.273	198.378
	Squared	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]	ATP6V1H	1377.1	46043.9	44666.8
	Rooted	lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214]	LRRC1	2.1616	71.6515	73.8131
3561	Measured	transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354]	TADA3L	203	8129.78	8332.78
	Ranked	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	DDB1	2.895	198.7	195.805
	Squared	vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034]	CUL5	1377	44776.4	43399.4
	Rooted	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	DLG2	2.1615	71.3363	73.4978
3562	Measured	neurofibromin (neurofibromatosis-related protein nf-1) [contains: neurofibromin truncated]. [swissprot;acc:p21359]	no value	202.9	8309.51	8512.41
	Ranked	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]	PCCB	2.895	198.7	195.805
	Squared	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706]	PTPN2	1376.1	47715.1	46339
	Rooted	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]	GRPEL1	2.1615	74.3363	76.4978
3563	Measured	nucleolar cysteine-rich protein; zinc finger autoantigen 330. [refseq;acc:nm_014487]	ZNF330	202.82	7808.7	8011.52
	Ranked	mitochondrial glutamate carrier 1. [refseq;acc:nm_024698]	SLC25A22	2.893	193.374	190.481
	Squared	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]	COX4I1	1375.3	44325.8	42950.5
	Rooted	nude nuclear distribution gene e homolog 1 (a. nidulans); lis1-interacting protein nude1, rat homolog. [refseq;acc:nm_017668]	NDE1	2.1606	73.4429	75.6035
3564	Measured	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352]	DLG4	202.8	7939.87	8142.67
	Ranked	coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618]	COPB1	2.893	199.657	196.764
	Squared	homolog of yeast long chain polyunsaturated fatty acid elongatio; homolog of yeast long chain polyunsaturated fatty acid elongation enzyme 2. [refseq;acc:nm_021814]	ELOVL5	1375.3	42448.6	41073.3

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.