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

Results: HTML CSV LaTeX

Showing element 1451 to 1500 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
182	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	Rooted	0	31.1565	35.6653	1.14471
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Ranked	1	277.546	240.461	1.15422
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	Ranked	0	11573.8	10231.3	1.13121
	rna-binding protein. [refseq;acc:nm_019027]	Measured	1	4069.83	5252.17	1.29051
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Rooted	1	57.45	66.332	1.1546
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Measured	0	971.889	794.63	1.22307
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Ranked	1	228.306	198.011	1.153
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	Squared		79779.8	108084	1.35478
	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Measured		4069.83	5252.17	1.29051
	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	Measured	0	375.07	306.727	1.22281
	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	Squared	0	37.9786	56.1843	1.47937
	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	Rooted	1	57.4586	66.3336	1.15446
	heat shock factor binding protein 1. [swissprot;acc:o75506]	Rooted	0	20.2359	17.6821	1.14443
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Ranked		11613	13133.5	1.13093
184	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Measured		375.07	306.727	1.22281
	calcyphosine. [swissprot;acc:q13938]	Rooted		18.8902	21.6141	1.1442
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted	1	153.602	133.195	1.15321
	ns1-associated protein 1. [refseq;acc:nm_006372]	Measured		4069.83	5252.17	1.29051
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Ranked		274.027	237.79	1.15239
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Ranked	0	6279.56	5569.42	1.12751
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Squared	1	72886.3	98544.5	1.35203
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Squared	0	4.23965	2.86829	1.47811
185	adiponectin receptor 2. [refseq;acc:nm_024551]	Ranked	1	281.582	246.371	1.14292
	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Squared	0	0.125207	0.0854438	1.46537
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Measured	0	375.322	306.933	1.22281
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Squared	1	41502.9	30836.8	1.34589
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Rooted	0	30.6682	26.8335	1.14291
	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Measured	1	4069.83	5252.17	1.29051
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Rooted	1	153.578	133.176	1.1532
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Ranked	0	6279.56	5569.42	1.12751
186	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Ranked		11935.1	10592.8	1.12672
	60s ribosomal protein l15. [swissprot;acc:p39030]	Rooted		19.482	17.0546	1.14233
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Measured	1	4071.1	5251.75	1.29001
	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]	Ranked	1	226.582	198.444	1.14179
	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	Measured	0	470.251	384.733	1.22228
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Squared	1	41502.9	30836.8	1.34589
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Squared	0	5086.87	3492.66	1.45645
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Rooted	1	153.578	133.176	1.1532
187	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Ranked	0	9955.22	11213.7	1.12641
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted	1	153.548	133.153	1.15317
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Squared	1	41502.9	30836.8	1.34589
	importin 9. [refseq;acc:nm_018085]	Measured	0	1143.55	1397.66	1.22221
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Ranked	1	226.582	198.444	1.14179
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Measured	1	4569.48	5885.79	1.28807
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Squared	0	8660.1	5963.73	1.45213
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Rooted		32.4121	28.377	1.1422
188	60s ribosomal protein l15. [swissprot;acc:p39030]	Ranked		11745.2	13203.1	1.12413
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Squared	1	41502.9	30836.8	1.34589
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Measured	0	1143.55	1397.66	1.22221
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Ranked	1	226.582	198.444	1.14179

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/