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.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1758 to 1807 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
220	mitochondrial ribosomal protein l2. [source:refseq;acc:nm_015950]	Ranked	Subtracted	242.339	266.986	24.647	
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Ranked	Divided	112	126	1.125	
220	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	Squared	Subtracted	57808.9	46630.3	11178.6	
221	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Measured	Divided	41482.5	33356.5	1.24361	
221	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Squared	Divided	70739	93908.8	1.32754	
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Ranked	Divided	112	126	1.125	
221	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Ranked	Subtracted	242.627	267.151	24.524	
221	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Measured	Subtracted	6417.18	7859.6	1442.42	
221	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Rooted	Subtracted	113.374	123.463	10.089	
221	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Rooted	Divided	56.9506	64.7888	1.13763	
221	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	Squared	Subtracted	57579.2	46497.2	11082	
222	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Ranked	Subtracted	242.153	266.673	24.52	
222	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Rooted	Divided	52.7936	60.0592	1.13762	
222	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Measured	Divided	41482.5	33356.5	1.24361	
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Ranked	Divided	112	126	1.125	
222	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Rooted	Subtracted	61.6639	71.7355	10.0716	
222	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	Squared	Subtracted	29570.7	18601.8	10968.9	
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	

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/