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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 891 to 940 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Ranked	112	126	1.125	
223	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Squared	40982.6	54272.3	1.32428	
224	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Measured	41482.5	33356.5	1.24361	
224	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Rooted	137.446	120.823	1.13758	
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	Ranked	185.969	165.623	1.12285	
224	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Squared	14943.9	19771.9	1.32307	
225	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Rooted	137.446	120.823	1.13758	
225	metaxin 1. [source:swissprot;acc:q13505]	Squared	60401.6	79875.7	1.32241	
225	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Measured	9035	7279.6	1.24114	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Ranked	226.471	201.769	1.12243	
226	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Ranked	239.991	269.238	1.12187	
226	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Rooted	137.446	120.823	1.13758	
226	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Measured	9035	7279.6	1.24114	
226	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	Squared	73510.2	55607.3	1.32195	
227	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Rooted	137.446	120.823	1.13758	
227	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Measured	9035	7279.6	1.24114	
227	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Squared	73995.1	56003.7	1.32125	
227	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Ranked	239.99	269.234	1.12186	
228	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	Squared	57913.5	76336.3	1.31811	
228	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Rooted	137.446	120.823	1.13758	
228	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Measured	9035	7279.6	1.24114	
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	Ranked	226.411	202.088	1.12036	
229	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Ranked	226.401	202.094	1.12028	
229	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Rooted	137.446	120.823	1.13758	
229	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). [source:swissprot;acc:p53778]	Squared	42411.6	55802.1	1.31573	
229	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Measured	9035	7279.6	1.24114	
230	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Ranked	239.35	267.915	1.11934	
230	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Measured	9035	7279.6	1.24114	
230	necdin. [source:swissprot;acc:q99608]	Rooted	137.446	120.823	1.13758	
230	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	Squared	42411.6	55802.1	1.31573	
231	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Ranked	239.336	267.881	1.11927	
231	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Rooted	137.446	120.823	1.13758	
231	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Measured	9035	7279.6	1.24114	
231	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [source:swissprot;acc:q9h3h5]	Squared	42411.6	55802.1	1.31573	
232	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Measured	9035	7279.6	1.24114	
232	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Rooted	137.446	120.823	1.13758	
232	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [source:swissprot;acc:q96qb1]	Squared	42411.6	55802.1	1.31573	
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Ranked	239.336	267.879	1.11926	
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	Ranked	239.32	267.842	1.11918	
233	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [source:swissprot;acc:p49137]	Squared	42411.6	55802.1	1.31573	
233	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Rooted	137.446	120.823	1.13758	
233	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Measured	9035	7279.6	1.24114	
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Ranked	287.41	256.835	1.11905	
234	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Rooted	137.446	120.823	1.13758	
234	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [source:swissprot;acc:q15825]	Squared	42411.6	55802.1	1.31573	
234	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Measured	5181.2	6410.58	1.23728	
235	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Rooted	137.446	120.823	1.13758	
235	nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	Squared	42411.6	55802.1	1.31573	
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	Ranked	227.357	254.15	1.11785	
235	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Measured	5181.2	6410.58	1.23728	

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/