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 1775 to 1824 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
222	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Measured	Subtracted	6417.18	7859.6	1442.42	
222	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [source:refseq;acc:nm_005843]	Squared	Divided	86281	65058.3	1.32621	
223	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Squared	Subtracted	29567	18601.6	10965.4	
223	cytohesin 4. [source:swissprot;acc:q9uia0]	Measured	Divided	41482.5	33356.5	1.24361	
223	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Rooted	Divided	137.446	120.823	1.13758	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Ranked	Divided	112	126	1.125	
223	septin 6. [source:swissprot;acc:q14141]	Rooted	Subtracted	113.169	123.23	10.061	
223	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Ranked	Subtracted	242.153	266.673	24.52	
223	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Squared	Divided	40982.6	54272.3	1.32428	
223	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Measured	Subtracted	6417.18	7859.59	1442.41	
224	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Ranked	Subtracted	242.153	266.673	24.52	
224	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Measured	Divided	41482.5	33356.5	1.24361	
224	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Rooted	Subtracted	44.849	54.7964	9.9474	
224	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	Squared	Subtracted	46021.4	56813.2	10791.8	
224	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Rooted	Divided	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	Divided	185.969	165.623	1.12285	
224	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Measured	Subtracted	6417.18	7859.59	1442.41	
224	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Squared	Divided	14943.9	19771.9	1.32307	
225	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	Measured	Subtracted	6417.19	7859.51	1442.32	
225	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Rooted	Divided	137.446	120.823	1.13758	
225	metaxin 1. [source:swissprot;acc:q13505]	Squared	Divided	60401.6	79875.7	1.32241	
225	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Measured	Divided	9035	7279.6	1.24114	
225	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	Squared	Subtracted	45986	56776.1	10790.1	
225	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Ranked	Subtracted	242.153	266.673	24.52	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Ranked	Divided	226.471	201.769	1.12243	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Rooted	Subtracted	55.7423	65.6839	9.9416	
226	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Ranked	Divided	239.991	269.238	1.12187	
226	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Measured	Subtracted	6417.31	7858.12	1440.81	
226	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Rooted	Divided	137.446	120.823	1.13758	
226	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Measured	Divided	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	Divided	73510.2	55607.3	1.32195	
226	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Ranked	Subtracted	242.153	266.673	24.52	
226	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]	Rooted	Subtracted	56.3447	66.124	9.7793	
226	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	Squared	Subtracted	45987	56777.1	10790.1	
227	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	Squared	Subtracted	45985.9	56776	10790.1	
227	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Rooted	Subtracted	56.3507	66.1252	9.7745	
227	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Measured	Subtracted	6417.33	7857.93	1440.6	
227	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Rooted	Divided	137.446	120.823	1.13758	
227	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Ranked	Subtracted	244.126	268.604	24.478	
227	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Measured	Divided	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	Divided	73995.1	56003.7	1.32125	
227	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Ranked	Divided	239.99	269.234	1.12186	
228	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	Squared	Subtracted	45986.7	56776.8	10790.1	
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	Divided	57913.5	76336.3	1.31811	
228	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Rooted	Divided	137.446	120.823	1.13758	
228	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Ranked	Subtracted	244.126	268.604	24.478	
228	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Rooted	Subtracted	95.0526	85.3206	9.732	
228	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Measured	Divided	9035	7279.6	1.24114	
228	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Measured	Subtracted	6417.81	7852.52	1434.71	
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	Divided	226.411	202.088	1.12036	

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/