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 2758 to 2807 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
345	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	Squared	0	354.23	402.944	1.13752
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Ranked	1	242.14	265.697	1.09729
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	Rooted	0	30.6431	29.1204	1.05229
346	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	Measured	0	1837.26	1721.76	1.06708
	40s ribosomal protein s3. [swissprot;acc:p23396]	Ranked	1	241.612	265.119	1.09729
	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Squared	0	176989	155919	1.13513
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Rooted	0	21.4045	20.3439	1.05213
	grb2-related adaptor protein. [swissprot;acc:q13588]	Rooted	1	61.4282	68.0107	1.10716
	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	Squared	1	34018.3	42373	1.24559
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Ranked	0	9267.81	9736.2	1.05054
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Measured	1	14229.2	16780.7	1.17931
347	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Measured	0	1491.75	1591.6	1.06693
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Ranked	0	7670	7311	1.0491
	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Rooted	1	66.4284	60.0004	1.10713
	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	Measured		4991.02	5885.09	1.17914
	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	Ranked		242.14	265.697	1.09729
	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Squared	0	10717.9	12115.3	1.13038
	scratch; scratch 1. [refseq;acc:nm_031309]	Rooted	0	21.5021	20.4389	1.05202
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Squared	1	16573.6	20637.8	1.24522
348	ad24 protein. [refseq;acc:nm_022451]	Rooted		49.2558	54.5235	1.10695
	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Ranked		242.14	265.696	1.09728
	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Measured	0	14357.1	13463.1	1.0664
	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	Squared	1	42566.2	52985.3	1.24477
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Ranked	0	16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Rooted		21.9882	20.9119	1.05147
	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	Measured	1	4991.02	5885.09	1.17914
349	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Rooted	0	15.4361	14.7003	1.05005
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Measured		957.833	898.833	1.06564
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	Measured	1	4714.85	5554.38	1.17806
	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	Squared		35533.9	44227	1.24464
	surfeit locus protein 5. [swissprot;acc:q15528]	Ranked		242.14	265.696	1.09728
	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Rooted		56.0061	61.9704	1.10649
350	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	Squared		35508.7	44191.4	1.24452
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Rooted	0	38.0352	36.2234	1.05002
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured		48	51	1.0625
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Ranked		16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Rooted	1	61.3383	67.8668	1.10643
	sedlin. [swissprot;acc:o14582]	Measured		17396.9	20483.9	1.17745
	zinc finger protein 291. [swissprot;acc:q9by12]	Ranked		242.14	265.696	1.09728
351	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	Rooted		61.3352	67.8618	1.10641
	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	Squared		35508.6	44191.3	1.24452
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Ranked	0	16321	15577	1.04776
		Squared		0.545325	0.615621	1.12891
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Measured		48	51	1.0625
	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	Ranked	1	242.14	265.696	1.09728
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	Rooted	0	24.5101	25.7223	1.04946

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/