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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Value Type Rank Gene description Interaction Map Network Comparison Type red Filtered green network_comparison

Results: HTML CSV LaTeX

Showing element 51 to 100 of 77072 in total

Value Type	Measured

Rank	description	Interaction Map	Network Comparison Type	red	Filtered	green	network_comparison	
7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Low confidence	Divided	736.5	1	2113.5	2.86965	
7	sedlin. [source:swissprot;acc:o14582]	High confidence	Divided	0.00001	0	43	4300000	
7	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	High confidence	Divided	1153.5	1	339.5	3.39764	
7	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	Low confidence	Divided	2.31962	0	0.00001	231962	
7	vitelliform macular dystrophy 2-like protein 1. [source:refseq;acc:nm_017682]	Low confidence	Subtracted	36360.3	1	43368.8	7008.5	
7	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	High confidence	Subtracted	13174.7	0	15605.1	2430.4	
8	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Low confidence	Divided	85	0	6410	75.4118	
8	db83 protein. [source:swissprot;acc:p57088]	High confidence	Divided	1153.5	1	339.5	3.39764	
8	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Low confidence	Subtracted	33111.4	1	39358.1	6246.7	
8	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	High confidence	Subtracted	5106.93	0	7500.75	2393.82	
8	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	High confidence	Subtracted	21185	1	28492	7307	
8	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [source:swissprot;acc:q07326]	Low confidence	Divided	3278	1	5058.5	1.54317	
8	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	High confidence	Divided	0.00001	0	43	4300000	
8	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Low confidence	Subtracted	7537.89	0	8770.72	1232.83	
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	High confidence	Subtracted	12478	0	14756	2278	
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Low confidence	Subtracted	10255.7	0	11468.3	1212.6	
9	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	High confidence	Divided	85	0	6410	75.4118	
9	n33 protein. [source:swissprot;acc:q13454]	Low confidence	Divided	3278	1	5058.5	1.54317	
9	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	High confidence	Subtracted	21185	1	28492	7307	
9	sperm associated antigen 7. [source:refseq;acc:nm_004890]	Low confidence	Subtracted	23318	1	19280.8	4037.2	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	High confidence	Divided	398.5	1	1281.5	3.21581	
9	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [source:swissprot;acc:o14607]	Low confidence	Divided	383.762	0	10.6048	36.1876	
10	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [source:sptrembl;acc:q9uge0]	Low confidence	Subtracted	1593	0	2804	1211	
10	implantation-associated protein. [source:refseq;acc:nm_032121]	Low confidence	Divided	3278	1	5058.5	1.54317	
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	High confidence	Divided	85	0	6410	75.4118	
10	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	High confidence	Subtracted	7830.62	0	6193.07	1637.55	
10	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	High confidence	Subtracted	21185	1	28492	7307	
10	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Low confidence	Subtracted	19498.1	1	17265.4	2232.7	
10	serpin b12. [source:swissprot;acc:q96p63]	Low confidence	Divided	199.549	0	5.56738	35.8425	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	High confidence	Divided	398.5	1	1281.5	3.21581	
11	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	High confidence	Subtracted	5734.28	0	7252.02	1517.74	
11	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Low confidence	Subtracted	4230.36	0	5341.81	1111.45	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	High confidence	Divided	398.5	1	1281.5	3.21581	
11	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	Low confidence	Divided	199.249	0	5.71669	34.8539	
11	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	High confidence	Subtracted	21185	1	28492	7307	
11	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Low confidence	Subtracted	7256.71	1	9368.87	2112.16	
11	serpin b12. [source:swissprot;acc:q96p63]	High confidence	Divided	199.549	0	5.56738	35.8425	
11	thyroid receptor interacting protein 8 (trip-8) (fragment). [source:swissprot;acc:q15652]	Low confidence	Divided	1917.64	1	2950.5	1.53861	
12	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	High confidence	Subtracted	5629.62	0	7099.51	1469.89	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	High confidence	Divided	398.5	1	1281.5	3.21581	
12	gbp protein isoform a. [source:refseq;acc:nm_017870]	Low confidence	Divided	1921.96	1	2954.24	1.5371	
12	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Low confidence	Subtracted	15464.1	1	17572.7	2108.6	
12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	High confidence	Divided	199.249	0	5.71669	34.8539	
12	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Low confidence	Divided	859	0	58	14.8103	
12	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	High confidence	Subtracted	34190.9	1	40795.8	6604.9	
12	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [source:swissprot;acc:o00268]	Low confidence	Subtracted	31122	0	30022.4	1099.6	
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	High confidence	Divided	1363	0	47	29	
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	High confidence	Subtracted	1363	0	47	1316	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	High confidence	Divided	398.5	1	1281.5	3.21581	
13	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [source:swissprot;acc:o75344]	Low confidence	Divided	8.11997	0	115.385	14.21	

Legend:
- Rank is the rank after comparing the two networks
- 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/