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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 7460 in total

Value Type	Measured
Interaction Map	High confidence

Rank	description	Network Comparison Type	red	Filtered	green	network_comparison	
1	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Subtracted	85	0	6410	6325	
1	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Subtracted	41482.5	1	33356.5	8126	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Divided	364	0	0.00001	36400000	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	450.5	1	2394.5	5.31521	
2	cab2. [source:refseq;acc:nm_033419]	Divided	0.00001	0	174	17400000	
2	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	41482.5	1	33356.5	8126	
2	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Subtracted	85	0	6410	6325	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	450.5	1	2394.5	5.31521	
3	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	41482.5	1	33356.5	8126	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	2597.5	1	698.5	3.71868	
3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Subtracted	23818.1	0	19621.3	4196.8	
3	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Divided	0.00001	0	109	10900000	
4	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	41482.5	1	33356.5	8126	
4	hbs1-like. [source:refseq;acc:nm_006620]	Divided	2597.5	1	698.5	3.71868	
4	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Divided	0.00001	0	89	8900000	
4	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Subtracted	18704	0	21730	3026	
5	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	41482.5	1	33356.5	8126	
5	histone h4. [source:swissprot;acc:p02304]	Subtracted	21773.1	0	24446.3	2673.2	
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Divided	0.00001	0	89	8900000	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	1153.5	1	339.5	3.39764	
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Divided	0.00001	0	89	8900000	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	1153.5	1	339.5	3.39764	
6	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	44490.5	1	36927.5	7563	
6	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Subtracted	13174.7	0	15605.1	2430.4	
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	21185	1	28492	7307	
7	sedlin. [source:swissprot;acc:o14582]	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]	Divided	1153.5	1	339.5	3.39764	
7	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Subtracted	13174.7	0	15605.1	2430.4	
8	db83 protein. [source:swissprot;acc:p57088]	Divided	1153.5	1	339.5	3.39764	
8	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	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]	Subtracted	21185	1	28492	7307	
8	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Divided	0.00001	0	43	4300000	
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Subtracted	12478	0	14756	2278	
9	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Divided	85	0	6410	75.4118	
9	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Subtracted	21185	1	28492	7307	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Divided	398.5	1	1281.5	3.21581	
10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	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]	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]	Subtracted	21185	1	28492	7307	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	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]	Subtracted	5734.28	0	7252.02	1517.74	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Divided	398.5	1	1281.5	3.21581	
11	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Subtracted	21185	1	28492	7307	
11	serpin b12. [source:swissprot;acc:q96p63]	Divided	199.549	0	5.56738	35.8425	
12	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Subtracted	5629.62	0	7099.51	1469.89	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Divided	398.5	1	1281.5	3.21581	
12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	Divided	199.249	0	5.71669	34.8539	
12	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Subtracted	34190.9	1	40795.8	6604.9	
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Divided	1363	0	47	29	
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Subtracted	1363	0	47	1316	

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/