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 1730 to 1779 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
217	human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	Squared	Subtracted	46785.7	58383.2	11597.5	
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Ranked	Divided	112	126	1.125	
217	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [source:swissprot;acc:p23284]	Squared	Divided	86600.9	65229.9	1.32763	
217	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Rooted	Divided	105.205	92.2415	1.14054	
217	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Measured	Subtracted	6417.18	7859.6	1442.42	
217	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [source:swissprot;acc:o15211]	Measured	Divided	16071.6	12886.8	1.24714	
217	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Rooted	Subtracted	121.695	131.815	10.12	
218	60s ribosomal protein l35. [source:swissprot;acc:p42766]	Ranked	Subtracted	242.333	266.999	24.666	
218	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Rooted	Divided	46.1476	52.5742	1.13926	
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Ranked	Divided	112	126	1.125	
218	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Measured	Subtracted	6417.18	7859.6	1442.42	
218	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	Rooted	Subtracted	107.178	117.276	10.098	
218	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	Measured	Divided	16070.4	12886	1.24712	
218	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	Squared	Divided	86600.9	65229.9	1.32763	
218	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [source:swissprot;acc:p15822]	Squared	Subtracted	46785.7	58383.2	11597.5	
219	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Ranked	Subtracted	242.339	266.986	24.647	
219	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	Squared	Divided	86600.9	65229.9	1.32763	
219	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Rooted	Subtracted	44.963	55.0576	10.0946	
219	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Rooted	Divided	52.7146	60.0088	1.13837	
219	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	Squared	Subtracted	46785.7	58383.2	11597.5	
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Ranked	Divided	112	126	1.125	
219	transforming protein n-ras. [source:swissprot;acc:p01111]	Measured	Divided	16069.8	12885.6	1.24711	
219	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Measured	Subtracted	6417.18	7859.6	1442.42	
220	brain protein 44. [source:swissprot;acc:o95563]	Rooted	Subtracted	113.374	123.463	10.089	
220	crk-like protein. [source:swissprot;acc:p46109]	Measured	Subtracted	6417.18	7859.6	1442.42	
220	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	Squared	Divided	86600.9	65229.9	1.32763	
220	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Measured	Divided	41482.5	33356.5	1.24361	
220	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Rooted	Divided	52.7557	60.035	1.13798	
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	

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/