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

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Showing element 373 to 422 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
24	fos-related antigen 2. [swissprot;acc:p15408]	Measured	Subtracted	0	3233.86	2208.1	1025.76
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Rooted	Divided	1	40.336	24.2941	1.66032
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Measured	Subtracted		23693.7	18263	5430.7
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Squared			219048	129762	89286
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Rooted		0	17.7955	7.34614	10.4494
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Rooted	Divided	0	29.3087	7.61577	3.84842
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Ranked		1	58	44	1.31818
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Measured			950.561	2108.52	2.21818
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Ranked	Subtracted		322	253	69
	ptd016 protein. [refseq;acc:nm_016125]	Measured	Divided	0	30	158	5.26667
	sedlin. [swissprot;acc:o14582]	Ranked	Subtracted		22440	16388	6052
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Squared	Subtracted		21101.4	11769.5	9331.9
25	60s ribosomal protein l37a. [swissprot;acc:p12751]	Squared	Divided		44.3683	0.344399	128.828
	60s ribosomal protein l37a. [swissprot;acc:p12751]	Rooted	Divided		13.7805	3.80565	3.62106
	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Measured	Subtracted		459.5	1377	917.5
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Squared	Divided	1	143.692	457.521	3.18404
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Ranked	Subtracted		322	253	69
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Rooted	Divided		40.3361	24.295	1.66026
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Measured			1833.01	892.67	2.0534
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Ranked		0	13730.5	8257	1.66289
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Squared	Subtracted	1	219048	129762	89286
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Measured			23693.7	18263	5430.7
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Rooted			146.94	167.046	20.106
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Ranked	Divided		58	44	1.31818
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Measured	Divided	0	148	773	5.22297
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Rooted	Subtracted		0	10.4403	10.4403
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Ranked			22440	16388	6052
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Squared			42556.5	33335.4	9221.1
26	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Squared	Divided		44.3683	0.344399	128.828
		Rooted			13.7805	3.80565	3.62106
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Ranked			12128.3	7533.33	1.60995
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Measured			153	662	4.3268
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Rooted	Subtracted		40.0375	29.9666	10.0709
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Rooted	Divided	1	40.3362	24.2954	1.66024
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Measured	Divided		1833.01	892.67	2.0534
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Measured	Subtracted		23693.7	18263	5430.7
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Squared			219048	129762	89286
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Ranked		0	11284	17173.8	5889.8
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Rooted		1	146.94	167.046	20.106
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Squared	Divided		143.692	457.521	3.18404
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Ranked	Divided		58	44	1.31818
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Ranked	Subtracted		322	253	69
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Squared		0	21273.2	12858.5	8414.7
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured			2965.5	2063	902.5
27	60s ribosomal protein l37a. [swissprot;acc:p12751]	Ranked			12941.7	18499.2	5557.5
	60s ribosomal protein l37a. [swissprot;acc:p12751]	Rooted			13.7805	3.80565	9.97485
	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Measured			14357.1	13463.1	894
	dystrophin. [swissprot;acc:p11532]	Rooted	Divided		17.8026	5.12693	3.47237
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Measured		1	1834.33	895.134	2.04922
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Rooted		1	40.3364	24.2968	1.66015

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.

- http://analysis.yellowcouch.org/