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 3051 to 3100 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
382	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Rooted	0	41.1548	39.6879	1.03696
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured	0	377.445	359.98	1.04852
	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Measured	1	4533.74	5279.4	1.16447
	rna-binding protein. [refseq;acc:nm_019027]	Squared	1	15043.7	18560.1	1.23375
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Squared	0	29631.4	32621.1	1.1009
	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Ranked	1	200.791	183.66	1.09328
383	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	Rooted		49.8325	45.2077	1.1023
	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Squared		15043.7	18560.1	1.23375
	chromodomain y-like protein 2. [refseq;acc:nm_152342]	Ranked	0	10273.1	10665.1	1.03816
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Measured	0	379.489	362.023	1.04825
	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	Measured	1	4533.74	5279.4	1.16447
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Rooted	0	42.25	43.7931	1.03652
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Squared	0	12235.5	13399.2	1.09511
	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	Ranked	1	237.862	217.739	1.09242
384	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Rooted	0	13.3606	12.8903	1.03648
	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Rooted	1	50.7723	46.0607	1.10229
	bystin. [swissprot;acc:q13895]	Ranked	0	10833.3	11244.5	1.03796
	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	Measured	1	4533.74	5279.4	1.16447
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Squared	0	79383.4	72701	1.09192
	ns1-associated protein 1. [refseq;acc:nm_006372]	Squared	1	15043.7	18560.1	1.23375
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Ranked	1	266.421	244.236	1.09083
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Measured	0	8243.06	8627.63	1.04665
385	40s ribosomal protein s28. [swissprot;acc:p25112]	Measured	0	387.486	405.367	1.04615
	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	Rooted	1	50.7723	46.0607	1.10229
	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Squared	1	15043.7	18560.1	1.23375
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Rooted	0	30.7569	31.8678	1.03612
	lamin b2. [swissprot;acc:q03252]	Squared	0	539.519	494.357	1.09136
	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Measured	1	4533.74	5279.4	1.16447
	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	Ranked	0	10302.7	10686.7	1.03727
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]		1	266.421	244.236	1.09083
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]			242.238	264.11	1.09029
	60s ribosomal protein l8. [swissprot;acc:p25120]	Measured		4533.74	5279.4	1.16447
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Rooted	0	39.0883	37.7357	1.03584
	mesoderm induction early response 1. [refseq;acc:nm_020948]	Squared		958.952	880.365	1.08927
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Measured		2156.64	2254.12	1.0452
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Rooted	1	50.0513	45.4124	1.10215
	scratch; scratch 1. [refseq;acc:nm_031309]	Squared	1	40388.9	49827.5	1.23369
	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	Ranked	0	10303.7	10687.4	1.03724
387	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Ranked	1	242.238	264.11	1.09029
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Rooted	1	50.3345	45.6718	1.10209
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Measured	0	1388.29	1330.37	1.04354
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Squared	1	15053	18568	1.23351
	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Measured	1	4533.74	5279.4	1.16447
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Rooted	0	29.6492	28.6255	1.03576
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Squared		12.0783	13.1443	1.08826
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Ranked		10481.8	10869.5	1.03699
388	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Squared	1	40315.7	49716.4	1.23318
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Ranked	0	9953.39	10320.9	1.03692
	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		34.4922	35.713	1.03539
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	Squared		948.513	872.867	1.08666

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/