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

Results: HTML CSV LaTeX

Showing element 59124 to 59173 of 66312 in total

Interaction Map

: Low confidence
Filtered

: 1

Rank	Hugo	Value Type	description	Network Comparison Type	red	green	network_comparison
4163	CSDE1	Rooted	unr protein. [swissprot;acc:o75534]	Divided	70.5777	72.3771	1.0255
	MLLT6	Squared	af-17 protein. [swissprot;acc:p55198]	Divided	42407.3	41318	1.02636
	PFDN1	Squared	prefoldin subunit 1. [swissprot;acc:o60925]	Subtracted	42835.1	41705.3	1129.8
	PSD3	Ranked	adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310]		200.724	198.625	2.099
	RECQL5	Measured	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]		7932.93	8110.32	177.39
4164	ANKRA2	Measured	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]		7826.11	8003.45	177.34
	CNTNAP3	Squared	contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]	Divided	42407.3	41318	1.02636
	FOXC2	Ranked	forkhead box protein c2 (forkhead-related protein fkhl14) (mesenchyme fork head protein 1) (mfh-1 protein) (transcription factor fkh-14). [swissprot;acc:q99958]		207.478	205.337	1.01043
	IFT122	Rooted	wd-repeat protein 10. [swissprot;acc:q9hbg6]		70.4306	72.2225	1.02544
	KIAA1012	Ranked	trs85 homolog. [swissprot;acc:q9y2l5]	Subtracted	200.724	198.625	2.099
	RERE	Measured	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]	Divided	7871.26	8033.99	1.02067
	SMOC2	Squared	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]	Subtracted	42835.1	41705.3	1129.8
	ZNF415	Rooted	zinc finger protein 415. [refseq;acc:nm_018355]	Subtracted	76.1821	78.0464	1.8643
4165	BCKDHB	Measured	2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953]	Divided	7871.26	8033.99	1.02067
	CCT6B	Ranked	t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [swissprot;acc:q92526]		199.886	197.823	1.01043
	CD151	Rooted	platelet-endothelial tetraspan antigen 3 (peta-3) (gp27) (membrane glycoprotein sfa-1) (cd151 antigen). [swissprot;acc:p48509]		70.282	72.0683	1.02542
	CHDH	Squared	choline dehydrogenase. [refseq;acc:nm_018397]	Subtracted	42835.1	41705.3	1129.8
	CXXC6	Ranked	leukemia-associated protein with a cxxc domain. [sptrembl;acc:q8nfu7]		200.724	198.625	2.099
	DZIP1	Measured	zinc finger daz interacting protein 1. [refseq;acc:nm_014934]		7912.61	8089.66	177.05
	MLLT10	Squared	af-10 protein. [swissprot;acc:p55197]	Divided	42407.3	41318	1.02636
	ZNF160	Rooted	zinc finger protein 347 (zinc finger 1111). [swissprot;acc:q96se7]	Subtracted	76.1821	78.0464	1.8643
4166	FOXC1	Ranked	forkhead box protein c1 (forkhead-related protein fkhl7) (forkhead- related transcription factor 3) (freac-3). [swissprot;acc:q12948]	Divided	207.478	205.337	1.01043
	PHACTR3	Measured	q9h4t4 like. [refseq;acc:nm_080672]	Subtracted	7899.2	8076.07	176.87
	PPP4C	Rooted	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172]	Divided	72.2841	74.1218	1.02542
	PSD4	Ranked	sec7 homolog; adp-ribosylation factor guanine nucleotide-exchange factor 6. [refseq;acc:nm_012455]	Subtracted	200.724	198.625	2.099
	PTBP1	Measured	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]	Divided	7871.26	8033.99	1.02067
	RAB8B	Squared	ras-related protein rab-8b. [swissprot;acc:q92930]	Divided	45686.8	44513.9	1.02635
	RRM2B	Squared	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Subtracted	45258.9	44129.4	1129.5
	ZNF16	Rooted	zinc finger protein clone 647. [swissprot;acc:p15622]	Subtracted	76.1821	78.0464	1.8643
4167	no value	Ranked	60s ribosomal protein l23a. [swissprot;acc:p29316]	Divided	207.351	209.511	1.01042
	CNNM2	Squared	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	Subtracted	47737.8	46608.7	1129.1
	DYNC2LI1	Rooted	dynein 2 light intermediate chain. [refseq;acc:nm_016008]	Divided	70.282	72.0683	1.02542
	EXOSC3	Measured	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	Divided	7705.98	7865.17	1.02066
	FLNB	Ranked	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Subtracted	190.559	188.462	2.097
	HOXA9	Squared	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	Divided	45548.3	44380.6	1.02631
	PIGS	Measured	gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52]	Subtracted	8045.49	8222.36	176.87
	ZNF282	Rooted	zinc finger protein 398 (zinc finger dna binding protein p52/p71). [swissprot;acc:q8td17]	Subtracted	76.182	78.0463	1.8643
4168	EYA4	Measured	eyes absent homolog 4. [swissprot;acc:o95677]	Divided	7873.07	8035.49	1.02063
	FOXJ1	Ranked	forkhead box protein j1 (forkhead-related protein fkhl13) (hepatocyte nuclear factor 3 forkhead homolog 4) (hfh-4). [swissprot;acc:q92949]	Subtracted	207.68	205.585	2.095
	HOXD9	Squared	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	Divided	45593.6	44425.2	1.0263
	LETM1	Ranked	leucine zipper-ef-hand containing transmembrane protein 1. [refseq;acc:nm_012318]	Divided	205.583	203.462	1.01042
	MAGI3	Measured	membrane-associated guanylate kinase-related 3. [refseq;acc:nm_152900]	Subtracted	7899.2	8076.07	176.87
	NEDD4L	Squared	ubiquitin-protein ligase nedd4-like; neural precursor cell expressed, developmentally down-regulated gene 4-like; potential epithelial sodium channel regulator; homolog of yeast ubiquitin-protein ligase rsp5. [refseq;acc:nm_015277]	Subtracted	45817	44688.2	1128.8
	NUMB	Rooted	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	Divided	70.6823	72.4769	1.02539
	ZNF35	Rooted	zinc finger protein 35 (zinc finger protein hf.10). [swissprot;acc:p13682]	Subtracted	76.1821	78.0464	1.8643
4169	no value	Ranked	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Subtracted	206.899	208.987	2.088
	no value	Squared	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	Divided	45583.4	44416.5	1.02627
	ACTR1A	Squared	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024]	Subtracted	45823	44694.5	1128.5
	EYA2	Measured	eyes absent homolog 2. [swissprot;acc:o00167]	Divided	7873.42	8035.66	1.02061
	POLR1C	Measured	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	Subtracted	7839.55	8016.1	176.55

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.

- http://analysis.yellowcouch.org/