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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 3030 to 3079 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
379	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Measured	1	6704.44	7811.45	1.16512
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	Squared	0	14693.6	16237.1	1.10505
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Rooted		28.9419	27.8832	1.03797
380	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	Ranked		9566.15	9936.37	1.0387
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	Measured	1	12998.5	15138.2	1.16461
	block 23. [sptrembl;acc:q8nhw5]	Squared	0	14555.7	16084.7	1.10504
	calcyphosine. [swissprot;acc:q13938]	Rooted	1	59.5128	65.604	1.10235
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	Measured	0	1927.62	1833.64	1.05125
	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	Squared	1	32991.5	40704.5	1.23379
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	Rooted	0	38.6064	40.0697	1.0379
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Ranked	1	242.109	264.79	1.09368
381	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Squared	0	49458.1	54614.9	1.10427
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Rooted		53.8801	55.9159	1.03778
	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	Measured		2509.05	2633.79	1.04972
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Rooted	1	59.5128	65.604	1.10235
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Measured		5246.01	6109.31	1.16456
	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	Squared		32987.4	40698.5	1.23376
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	Ranked	0	9565.54	9935.19	1.03864
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Ranked	1	200.586	183.423	1.09357
382	40s ribosomal protein s23. [swissprot;acc:p39028]	Rooted	1	49.8325	45.2077	1.1023
	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	Ranked	0	10449	10061.8	1.03848
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Rooted		41.1548	39.6879	1.03696
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured		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

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/