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 4458 to 4507 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
279	mosaic protein lgn. [swissprot;acc:p81274]	Measured	Divided	1	3119.98	2579.49	1.20953
	musashi 2 isoform a. [refseq;acc:nm_138962]	Squared			15569.5	19953.6	1.28158
	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	Rooted			66.0989	74.0609	1.12046
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Ranked	Subtracted	0	7621.99	8473.85	851.86
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Measured		0	184.422	88.5622	95.8598
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Measured		1	4771.21	5961.43	1190.22
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	Ranked			242.66	265.715	23.055
280	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	Squared			30566.4	38866.5	8300.1
	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Squared	Divided	0	29812	36822.7	1.23516
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Rooted		1	57.9068	64.8562	1.12001
	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	Rooted		0	28.8531	26.484	1.08945
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Ranked			10620.1	11471.2	1.08014
		Ranked	Subtracted		10620.1	11471.2	851.1
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Measured			578.056	482.7	95.356
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Rooted		1	42.0577	50.424	8.3663
	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Rooted		0	26.1236	28.1011	1.9775
	metastasis-associated protein mta1. [swissprot;acc:q13330]	Ranked	Divided	1	252.512	228.356	1.10578
	musashi 1. [refseq;acc:nm_002442]	Squared		1	15569.5	19953.6	1.28158
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Measured		0	545.902	610.424	1.11819
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]		Subtracted	1	677.5	1865.5	1188
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]		Divided	1	3119.98	2579.49	1.20953
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	Squared	Subtracted	0	618.307	511.996	106.311
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Ranked		1	267.208	244.168	23.04
281	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]				242.159	265.104	22.945
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]		Divided		241.808	267.335	1.10557
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]		Subtracted	0	11096.8	10251.6	845.2
	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	Measured		0	1927.62	1833.64	93.98
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Rooted		1	42.0684	50.4323	8.3639
	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]	Measured	Divided	1	3119.98	2579.49	1.20953
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Rooted	Subtracted	0	4.28588	6.23127	1.94539
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Measured	Subtracted	1	677.5	1865.5	1188
	nuclear protein ukp68. [refseq;acc:nm_024824]	Squared	Divided	1	15569.5	19953.6	1.28158
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Ranked		0	12522.7	13514.5	1.0792
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Squared			4275.32	3463.45	1.23441
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Squared	Subtracted		17185.8	17080.7	105.1
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Rooted	Divided		27.1299	29.5494	1.08918
	t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	Squared	Subtracted	1	52623.3	44380.3	8243
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	Measured	Divided	0	545.902	610.424	1.11819
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	Rooted	Divided	1	57.9068	64.8562	1.12001
282	40s ribosomal protein s3a. [swissprot;acc:p49241]	Squared	Subtracted	0	8653.02	8550.86	102.16
	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Ranked	Divided	1	252.39	228.297	1.10553
	double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]	Squared	Subtracted	1	52623.3	44380.3	8243
	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	Ranked	Subtracted	0	10735.1	9891.37	843.73
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Rooted	Divided		25.5082	23.4377	1.08834
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	Measured	Subtracted		1927.62	1833.64	93.98
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	Ranked	Subtracted	1	242.159	265.104	22.945
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	Measured	Divided	0	178.955	199.751	1.11621
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Measured	Subtracted	1	677.5	1865.5	1188
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Squared	Divided	0	8755.38	7114.89	1.23057
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Measured	Divided	1	3119.98	2579.49	1.20953

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/