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 2625 to 2674 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
329	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Squared	0	195397	170319	1.14724
	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	Rooted	1	50.3803	45.4193	1.10923
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Measured	0	1658.07	1805.36	1.08883
	metaxin 2. [swissprot;acc:o75431]	Squared	1	41236	51807	1.25635
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Ranked		312	284	1.09859
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Measured		15999.1	19007.1	1.18801
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	Ranked	0	15977.3	15115.5	1.05701
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Rooted		15.4404	16.3116	1.05642
330	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Measured		1658.23	1805.52	1.08882
	60s ribosomal protein l32. [swissprot;acc:p02433]	Rooted	1	50.519	45.5497	1.1091
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Ranked	1	312	284	1.09859
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted	0	57.5016	60.7262	1.05608
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Squared	0	2758.07	3161.7	1.14635
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Squared	1	16203.4	20339.9	1.25529
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Ranked	0	12320.2	13018.5	1.05668
	septin 6. [swissprot;acc:q14141]	Measured	1	15959.9	18957.1	1.1878
331	40s ribosomal protein s3a. [swissprot;acc:p49241]	Ranked	0	10405.1	10992.4	1.05644
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Squared		26.2121	22.8932	1.14497
	alpha-nac protein. [sptrembl;acc:q9h009]	Rooted		9.95878	9.44328	1.05459
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Rooted	1	60.6697	67.2802	1.10896
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Ranked	1	312	284	1.09859
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Measured	0	4088	4451	1.0888
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Measured	1	20287.2	17083.8	1.18751
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Squared	1	33100.3	41520.6	1.25439
332	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Measured	0	15411.3	14167	1.08783
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Rooted		15.297	14.5086	1.05434
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Squared		3693.52	3232.47	1.14263
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Ranked		8125.5	7697.5	1.0556
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Ranked	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
333	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Rooted	0	105.939	111.683	1.05422
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Squared		3680.39	3222.57	1.14207
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Ranked		8125.5	7697.5	1.0556
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Ranked	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
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	Squared	1	64975.9	81151.2	1.24894
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Rooted	0	10.603	10.0581	1.05418
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Squared		3680.47	3222.63	1.14207
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Ranked		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
	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		14924.4	17655.2	1.18298
335	40s ribosomal protein s11. [swissprot;acc:p04643]	Rooted		50.4705	45.5342	1.10841
335	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	1.05406

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/