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

Results: HTML CSV LaTeX

Showing element 7412 to 7461 of 25824 in total

Filtered  : 1
Interaction Map  : High confidence

Rank	Network Comparison Type	description	Value Type	green	network_comparison	red
927	Divided	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437]	Rooted	65.7019	1.05899	62.0422
	Subtracted	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	Squared	27309.8	3651.3	23658.5
		dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]	Rooted	66.0327	3.671	62.3617
		splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Ranked	212.618	7.628	220.246
		swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]	Measured	4691.24	556.47	4134.77
928	Divided	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1]		6194.04	1.09853	5638.46
		gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]	Rooted	65.7019	1.05899	62.0422
		peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Ranked	218.017	1.03651	225.976
		squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	Squared	23904.8	1.15565	20685.1
	Subtracted	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]	Rooted	66.0328	3.671	62.3618
		phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393]	Squared	28800.9	3649.1	25151.8
		splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	Ranked	212.618	7.628	220.246
		swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]	Measured	4691.24	556.47	4134.77
929	Divided	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	Ranked	218.015	1.03642	225.955
		surfeit locus protein 1. [swissprot;acc:q15526]	Measured	6194.04	1.09853	5638.46
		tubulin-tyrosine ligase. [refseq;acc:nm_153712]	Squared	26143	1.15543	22626.3
		vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Rooted	66.0327	1.05887	62.3617
	Subtracted	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	Ranked	235.422	7.623	243.045
		argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966]	Squared	28625.4	3648.5	24976.9
		swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Measured	4691.24	556.47	4134.77
		vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8]	Rooted	66.0328	3.671	62.3618
930	Divided	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]		66.0327	1.05887	62.3617
		dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Measured	6194.23	1.09853	5638.65
		homolog of yeast maf1. [refseq;acc:nm_032272]	Squared	30074.5	1.1554	26029.5
		pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	Ranked	239.778	1.0364	231.357
	Subtracted	homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622]	Measured	6837.61	556.4	6281.21
		phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939]	Squared	28821.7	3641.5	25180.2
		programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	Ranked	225.782	7.62	233.402
		secretory pathway component sec31b-1. [refseq;acc:nm_015490]	Rooted	66.0328	3.671	62.3618
931	Divided	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Ranked	164.917	1.03637	159.13
		sec13-related protein. [swissprot;acc:p55735]	Rooted	66.0328	1.05887	62.3618
		seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]	Measured	6194.17	1.09853	5638.59
		tumor differentially expressed protein 2. [refseq;acc:nm_178865]	Squared	30074.5	1.1554	26029.5
	Subtracted	cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]	Measured	6837.61	556.4	6281.21
		kinesin family member c3. [refseq;acc:nm_005550]	Squared	30597.1	3639.1	26958
		prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	Ranked	221.421	7.532	228.953
		vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]	Rooted	66.0327	3.671	62.3617
932	Divided	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]	Measured	6194.04	1.09853	5638.46
		mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	Ranked	218.013	1.03636	225.939
		tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]	Squared	30074.5	1.1554	26029.5
		vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4]	Rooted	66.0327	1.05887	62.3617
	Subtracted	activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]	Measured	6837.61	556.4	6281.21
		prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]	Ranked	221.421	7.532	228.953
		upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	Squared	31646.5	3636.5	28010
		vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864]	Rooted	66.0297	3.6709	62.3588
933	Divided	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	Ranked	164.951	1.03635	159.165
		protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]	Measured	6194.04	1.09853	5638.46
		tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]	Squared	30074.5	1.1554	26029.5
		vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]	Rooted	66.0328	1.05887	62.3618
	Subtracted	cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569]	Measured	6837.61	556.4	6281.21

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.