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

Results: HTML CSV LaTeX

Showing element 2801 to 2850 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
701	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Squared	25852.2	30258.6	1.17045	
701	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	Ranked	220.438	209.118	1.05413	
701	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	Measured	7802.31	8731.82	1.11913	
701	ras-related protein rab-37. [source:swissprot;acc:q96ax2]	Rooted	51.4945	48.0189	1.07238	
702	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	Ranked	220.438	209.118	1.05413	
702	ras-related protein rab-26. [source:swissprot;acc:q9ulw5]	Rooted	51.4945	48.0189	1.07238	
702	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	Measured	7067.46	7909.27	1.11911	
702	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [source:swissprot;acc:p27449]	Squared	25114	29386	1.1701	
703	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [source:swissprot;acc:p19387]	Rooted	51.4945	48.0189	1.07238	
703	limkain b1. [source:refseq;acc:nm_019081]	Ranked	220.438	209.118	1.05413	
703	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Measured	6912.56	7735.12	1.11899	
703	sarcoglycan zeta; zeta-sarcoglycan. [source:refseq;acc:nm_139167]	Squared	25114	29386	1.1701	
704	alpha-nac protein. [source:sptrembl;acc:q9h009]	Measured	6912.27	7734.68	1.11898	
704	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [source:refseq;acc:nm_022735]	Squared	25114	29386	1.1701	
704	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	Ranked	220.438	209.118	1.05413	
704	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Rooted	57.2102	53.3508	1.07234	
705	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	Ranked	220.438	209.118	1.05413	
705	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	Squared	25114	29386	1.1701	
705	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Measured	6912.09	7734.41	1.11897	
705	syntaxin 6. [source:swissprot;acc:o43752]	Rooted	57.2202	53.3639	1.07226	
706	cellular modulator of immune recognition. [source:refseq;acc:nm_145021]	Squared	25114	29386	1.1701	
706	di-ras2. [source:refseq;acc:nm_017594]	Measured	6912.08	7734.39	1.11897	
706	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	Ranked	220.438	209.118	1.05413	
706	signal recognition particle 68 kda protein (srp68). [source:swissprot;acc:q9uhb9]	Rooted	60.6572	64.9858	1.07136	
707	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	Measured	5317.78	5944.25	1.11781	
707	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	Ranked	220.438	209.118	1.05413	
707	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Rooted	74.8348	80.1352	1.07083	
707	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	Squared	25114	29386	1.1701	
708	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Ranked	220.438	209.118	1.05413	
708	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Rooted	74.8348	80.1352	1.07083	
708	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	Squared	19970	23366.8	1.1701	
708	z-protein (protein cgi-119) (s1r protein). [source:swissprot;acc:q9hc24]	Measured	5317.78	5944.25	1.11781	
709	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	Ranked	220.438	209.118	1.05413	
709	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	Squared	25114	29386	1.1701	
709	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Rooted	80.4069	86.1018	1.07083	
709	pp1201 protein. [source:refseq;acc:nm_022152]	Measured	5317.78	5944.25	1.11781	
710	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	Ranked	220.438	209.118	1.05413	
710	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	Measured	5317.78	5944.25	1.11781	
710	ring finger protein 25 (ec 6.3.2.-). [source:swissprot;acc:q96bh1]	Squared	51519.3	44060.4	1.16929	
710	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	Rooted	69.2869	74.1856	1.0707	
711	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	Rooted	58.3914	62.5196	1.0707	
711	hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [source:swissprot;acc:q9nzj6]	Squared	25626.4	29950.3	1.16873	
711	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	Measured	5317.78	5944.25	1.11781	
711	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [source:swissprot;acc:p54577]	Ranked	232.468	245.048	1.05411	
712	atp synthase coupling factor b, mitochondrial precursor. [source:swissprot;acc:q99766]	Squared	25626.4	29950.3	1.16873	
712	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	Ranked	220.431	209.123	1.05407	
712	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [source:swissprot;acc:p36956]	Measured	5317.78	5944.25	1.11781	
712	vinculin (metavinculin). [source:swissprot;acc:p18206]	Rooted	62.9163	67.3603	1.07063	
713	dendritic cell protein. [source:refseq;acc:nm_006360]	Ranked	223.121	211.685	1.05402	
713	guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [source:swissprot;acc:q9y2t3]	Squared	25626.4	29950.3	1.16873	

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/