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 6858 to 6907 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
429	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Squared	Divided	1	29101.9	35347	1.21459
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared	Subtracted	0	0	2.81207	2.81207
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Measured			18	0	18
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Ranked			11621.7	11913.4	291.7
	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]	Measured	Divided		472.351	485.852	1.02858
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Squared			4841.65	4659.88	1.03901
	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	Measured		1	6272.91	7226.06	1.15195
430	40s ribosomal protein s28. [swissprot;acc:p25112]	Measured	Subtracted	0	387.486	405.367	17.881
	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Squared	Divided	1	29098.8	35342.6	1.21457
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Squared	Subtracted		33104	38818.5	5714.5
	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	Measured			6739.82	7644.63	904.81
	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	Rooted			66.082	71.6526	5.5706
	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Squared		0	9.56237	6.91035	2.65202
	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	Ranked		0	21205	20914	291
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Rooted	Divided	1	54.4927	49.6125	1.09837
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]		Divided	0	22.1458	22.7768	1.02849
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]		Subtracted		9.92736	9.42407	0.50329
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Ranked	Divided		11621.7	11913.4	1.0251
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Measured	Divided		10247.8	10535	1.02803
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	Ranked	Subtracted	1	250.938	234.134	16.804
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Measured	Divided	1	3804.09	4379.37	1.15123
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Squared		0	366.279	352.536	1.03898
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Ranked		1	227.748	210.888	1.07995
431	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	Ranked	Subtracted		233.529	216.737	16.792
	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Measured	Divided		3849.94	4431.36	1.15102
	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	Rooted	Subtracted	0	22.2195	22.7215	0.502
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]		Divided	1	54.4927	49.6125	1.09837
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]		Subtracted		66.082	71.6526	5.5706
	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]	Measured	Subtracted		6739.82	7644.63	904.81
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Ranked	Divided	0	10043.7	9799.17	1.02495
	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	Ranked	Subtracted		21205	20914	291
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Squared	Divided		14421.3	14982.3	1.0389
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Measured	Divided		146.622	150.709	1.02787
	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	Squared	Subtracted	1	33104	38818.5	5714.5
	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	Squared		0	9.56237	6.91035	2.65202
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Measured		0	93.5	111	17.5
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared	Divided	1	29096	35338.7	1.21456
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Rooted		0	25.6478	26.3666	1.02803
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Ranked		1	236.245	255.113	1.07987
432	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Squared	Subtracted	0	0.849445	3.43037	2.58092
	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]		Divided	1	29095.3	35337.6	1.21455
	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]		Subtracted		26598.9	32283.5	5684.6
	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	Ranked	Divided		212.547	229.411	1.07934
	fibrillin 3. [refseq;acc:nm_032447]	Ranked	Divided	0	930	953	1.02473
	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	Rooted	Subtracted	1	66.082	71.6526	5.5706
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Squared	Divided	0	25936.7	26909.5	1.03751
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Measured	Subtracted		379.489	362.023	17.466
	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Measured	Divided		100.5	103.25	1.02736
	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]	Ranked	Subtracted		21205	20914	291
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Rooted	Divided	1	54.4927	49.6125	1.09837

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/