MK5 Microarray Data

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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 6908 to 6957 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	Network Comparison Type	description	network_comparison	red	green
864	Ranked	Subtracted	exocyst complex component sec8. [swissprot;acc:q96a65]	8.313	217.762	209.449
	Squared	Divided	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]	1.16025	24242.8	28127.6
		Subtracted	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526]	3842	22245.5	26087.5
	Rooted	Divided	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]	1.06202	62.7551	66.6474
		Subtracted	exocyst complex component sec8. [swissprot;acc:q96a65]	3.8439	63.2983	67.1422
865	Measured	Divided	phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986]	1.10322	5595.65	6173.23
		Subtracted	15 kda selenoprotein precursor. [swissprot;acc:o60613]	588.95	6344.41	6933.36
	Ranked	Divided	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	1.03997	211.961	203.814
		Subtracted	zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	8.276	269.963	278.239
	Squared	Divided	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]	1.16025	24242.8	28127.6
		Subtracted	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	3841.5	26583.7	30425.2
	Rooted	Divided	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]	1.06202	62.7551	66.6474
		Subtracted	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	3.8407	62.2332	58.3925
866	Measured	Divided	ring finger protein 38. [refseq;acc:nm_022781]	1.10322	5595.65	6173.23
		Subtracted	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	588.13	4510.61	5098.74
	Ranked	Divided	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	1.03994	221.306	212.806
		Subtracted	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	8.272	269.96	278.232
	Squared	Divided	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]	1.16025	24242.8	28127.6
		Subtracted	esterase d (ec 3.1.1.1). [swissprot;acc:p10768]	3841.5	26583.7	30425.2
	Rooted	Divided	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	1.06163	51.8306	55.0247
		Subtracted	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	3.8359	62.5007	58.6648
867	Measured	Divided	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]	1.10322	5595.65	6173.23
		Subtracted	rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	587.7	6545.19	7132.89
	Ranked	Divided	40s ribosomal protein s3a. [swissprot;acc:p49241]	1.03981	225.689	234.674
		Subtracted	zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	8.267	269.956	278.223
	Squared	Divided	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]	1.16025	24242.8	28127.6
		Subtracted	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	3829	19263.3	23092.3
	Rooted	Divided	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	1.06137	61.668	65.4526
		Subtracted	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	3.8286	64.1165	67.9451
868	Measured	Divided	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]	1.10322	5595.65	6173.23
		Subtracted	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747]	587.55	5607.43	6194.98
	Ranked	Divided	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	1.03975	233.298	242.571
		Subtracted	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	8.267	269.956	278.223
	Squared	Divided	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	1.16023	31099.4	36082.4
		Subtracted	syntaxin 6. [swissprot;acc:o43752]	3827.9	26720.4	30548.3
	Rooted	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	1.06137	61.668	65.4526
		Subtracted	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	3.8283	64.1184	67.9467
869	Measured	Divided	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]	1.10322	5595.65	6173.23
		Subtracted	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456]	586.8	6540.61	7127.41
	Ranked	Divided	exocyst complex component sec8. [swissprot;acc:q96a65]	1.03969	217.762	209.449
		Subtracted	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	8.266	269.955	278.221
	Squared	Divided	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	1.16022	20273.1	23521.2
		Subtracted	syntaxin 10 (syn10). [swissprot;acc:o60499]	3819.7	26702.8	30522.5
	Rooted	Divided	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	1.06137	61.668	65.4526
		Subtracted	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	3.8109	100.26	96.4491
870	Measured	Divided	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]	1.10322	5595.65	6173.23
		Subtracted	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]	582.8	6390.28	6973.08
	Ranked	Divided	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	1.03962	211.908	203.832
		Subtracted	zinc finger protein 305. [swissprot;acc:o43309]	8.265	269.954	278.219
	Squared	Divided	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	1.16019	21086.3	24464.1

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.