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

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Showing element 5308 to 5357 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Ranked	Divided	1	312	284	1.09859
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Squared			14464.3	18142.8	1.25432
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Measured			5051.16	5975.51	1.183
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Rooted			60.6732	67.2827	1.10894
	vav-2 protein. [swissprot;acc:p52735]	Measured	Subtracted		6660.02	7697.78	1037.76
333	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	Rooted		0	24.2756	25.588	1.3124
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]			1	95.4476	102.785	7.3374
	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]		Divided	0	105.939	111.683	1.05422
	deltex 2. [refseq;acc:nm_020892]	Measured	Subtracted	1	1618.84	2651.88	1033.04
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Squared	Subtracted	0	2403.2	2359.13	44.07
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]		Divided	0	3680.39	3222.57	1.14207
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]		Subtracted	1	19321	12542.6	6778.4
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Ranked	Divided	0	8125.5	7697.5	1.0556
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Measured	Subtracted	0	545.902	610.424	64.522
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Ranked	Divided	1	312	284	1.09859
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Measured			5039.63	5961.83	1.18299
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Rooted			49.0526	54.3781	1.10857
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Squared			14464.3	18142.8	1.25432
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Measured		0	634.305	584.237	1.0857
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Ranked	Subtracted	0	8095.69	8732.68	636.99
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Ranked		1	265.634	244.304	21.33
334	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Rooted		0	27.6061	28.9062	1.3001
	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Ranked		0	10253.5	9622.45	631.05
	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	Squared	Divided	1	64975.9	81151.2	1.24894
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Measured	Subtracted	1	1629.21	2662.12	1032.91
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Rooted	Divided	0	10.603	10.0581	1.05418
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Squared	Subtracted	0	2400.71	2356.66	44.05
	e-1 enzyme. [refseq;acc:nm_021204]		Subtracted	1	30903.8	37638.1	6734.3
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]		Divided	0	3680.47	3222.63	1.14207
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Ranked		0	8125.5	7697.5	1.0556
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Ranked		1	312	284	1.09859
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Measured		0	3161.12	2924.8	1.0808
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Rooted		1	58.6096	64.9655	1.10844
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Ranked	Subtracted		232.473	211.207	21.266
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Measured	Divided		14924.4	17655.2	1.18298
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	Measured	Subtracted	0	545.902	610.424	64.522
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Rooted		1	58.2964	65.5926	7.2962
335	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]			0	30.7424	32.0298	1.2874
	40s ribosomal protein s11. [swissprot;acc:p04643]		Divided	1	50.4705	45.5342	1.10841
	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]		Divided	0	24.2756	25.588	1.05406
	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	Squared	Subtracted	1	30924.3	37652.3	6728
	60s ribosomal protein l37a. [swissprot;acc:p12751]	Squared	Subtracted	0	44.3683	0.344399	44.0239
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Ranked	Divided	1	312	284	1.09859
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Measured	Subtracted	0	4158.33	4094.09	64.24
	germ cell-less. [refseq;acc:nm_022471]	Measured	Divided	0	1829.81	1694.05	1.08014
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Rooted	Subtracted	1	52.7146	60.0088	7.2942
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Squared	Divided	0	3680.43	3222.6	1.14207
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Ranked	Subtracted	1	223.273	202.423	20.85
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Ranked	Divided	0	8125.5	7697.5	1.0556
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Measured	Divided	1	3494.31	4129.6	1.18181

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/