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 3001 to 3050 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
376	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Rooted	0	32.3671	31.1453	1.03923
	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Rooted	1	50.2554	45.5688	1.10285
	44050 protein. [refseq;acc:nm_178832]	Measured		17385.9	14889.2	1.16769
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Squared		46021.4	56813.2	1.2345
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Squared	0	1062.18	952.74	1.11487
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Ranked	1	257.017	234.945	1.09395
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Measured	0	4912.01	4658.69	1.05438
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Ranked		10284.9	10695.6	1.03993
377	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Rooted		45.8794	47.6722	1.03908
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Measured		884.254	931.405	1.05332
	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Squared		570.099	634.654	1.11323
	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	Ranked	1	242.691	265.481	1.09391
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Ranked	0	14512.3	13958.2	1.0397
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Rooted	1	50.2554	45.5687	1.10285
	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	Measured		17385.9	14889.2	1.16769
	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	Squared		33044.9	40781.4	1.23412
378	60s ribosomal protein l30. [swissprot;acc:p04645]	Ranked		242.593	265.365	1.09387
	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	Measured	0	703.068	739.623	1.05199
	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Rooted	0	74.2677	71.5378	1.03816
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Squared	1	15034.5	18552.2	1.23398
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Measured		12471.7	14561.7	1.16758
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	Rooted		50.5816	45.8738	1.10263
	neurocalcin delta. [swissprot;acc:p29554]	Squared	0	4946.59	5466.65	1.10514
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Ranked		19713.5	18962.5	1.0396
379	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]			11228.4	10806	1.03909
	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]		1	241.509	264.163	1.0938
	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	Squared	1	33010.8	40732.2	1.23391
	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	Measured	0	1927.62	1833.64	1.05125
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Rooted	1	59.5128	65.604	1.10235
	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
382	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	Ranked	0	10449	10061.8	1.03848

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/