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 1800 to 1849 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Ranked	1	226.471	201.769	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Ranked	1	239.991	269.238	1.12187
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Measured	0	658.544	758.411	1.15165
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Measured		9035	7279.6	1.24114
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Squared		73510.2	55607.3	1.32195
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Ranked	0	15395.7	16992.9	1.10374
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Rooted		30.2675	34.1662	1.12881
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	Squared		399.199	542.77	1.35965
227	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Squared		1662.68	2253.78	1.35551
	integral membrane protein cii-3b. [sptrembl;acc:o75609]	Rooted		19.6188	22.1086	1.12691
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Rooted	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Measured		9035	7279.6	1.24114
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Squared		73995.1	56003.7	1.32125
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Ranked		239.99	269.234	1.12186
	tigger transposable element derived 6. [refseq;acc:nm_030953]	Ranked	0	12360	11200.2	1.10355
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Measured	0	424.258	369.011	1.14972
228	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Squared	1	57913.5	76336.3	1.31811
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Rooted	1	137.446	120.823	1.13758
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	Rooted	0	25.4117	22.5968	1.12457
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Measured	1	9035	7279.6	1.24114
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	Squared	0	8107.36	10981.2	1.35447
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Ranked	1	226.411	202.088	1.12036
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Measured	0	4089.65	4696.36	1.14835
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Ranked	0	10303.5	11370.4	1.10355
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Ranked	1	226.401	202.094	1.12028
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Rooted	0	22.2195	19.7836	1.12313
	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	Measured		320.752	368.317	1.14829
	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	Squared		447.465	604.018	1.34987
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Rooted	1	137.446	120.823	1.13758
	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	Squared		42411.6	55802.1	1.31573
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Measured		9035	7279.6	1.24114
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Ranked	0	10899.4	9878.1	1.10339
230	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Rooted	0	35.3509	31.4916	1.12255
	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	Ranked	1	239.35	267.915	1.11934
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Measured		9035	7279.6	1.24114
	necdin. [swissprot;acc:q99608]	Rooted		137.446	120.823	1.13758
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Squared	0	82802.3	111762	1.34975
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	Squared	1	42411.6	55802.1	1.31573
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Ranked	0	12364.7	11207.7	1.10323
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Measured		1498.17	1718.6	1.14713
231	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Measured		2017.91	1759.22	1.14705
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Rooted		25.0015	28.0435	1.12167
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Ranked	1	239.336	267.881	1.11927
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Rooted		137.446	120.823	1.13758
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Measured		9035	7279.6	1.24114
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Squared	0	1914.2	1419.67	1.34834
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Ranked	0	12364.8	11207.9	1.10322
	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	Squared	1	42411.6	55802.1	1.31573
232	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	Squared	0	0.108639	0.145878	1.34278

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/