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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

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 2477 to 2526 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1239	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	Divided	219.354	224.699	1.02437	
1239	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	Subtracted	222.573	227.751	5.178	
1240	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	Divided	219.354	224.7	1.02437	
1240	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	Subtracted	222.574	227.752	5.178	
1241	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	Divided	219.354	224.7	1.02437	
1241	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	Subtracted	222.573	227.75	5.177	
1242	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	Divided	219.354	224.7	1.02437	
1242	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Subtracted	162.055	156.884	5.171	
1243	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	Divided	219.354	224.699	1.02437	
1243	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	Subtracted	222.569	227.739	5.17	
1244	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	Divided	219.354	224.7	1.02437	
1244	tumor protein d53 (hd53) (d52-like 1). [source:swissprot;acc:q16890]	Subtracted	206.774	211.936	5.162	
1245	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]	Divided	219.354	224.699	1.02437	
1245	tumor protein d52 (n8 protein). [source:swissprot;acc:p55327]	Subtracted	206.771	211.926	5.155	
1246	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	Divided	219.354	224.699	1.02437	
1246	sestrin 3. [source:swissprot;acc:p58005]	Subtracted	218.368	213.219	5.149	
1247	sestrin 2 (hi95). [source:swissprot;acc:p58004]	Subtracted	218.368	213.219	5.149	
1247	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	Divided	219.354	224.7	1.02437	
1248	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [source:swissprot;acc:q02928]	Subtracted	218.368	213.22	5.148	
1248	keratin associated protein 4.4. [source:refseq;acc:nm_032524]	Divided	219.354	224.699	1.02437	
1249	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	Divided	219.354	224.7	1.02437	
1249	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:q08477]	Subtracted	218.368	213.22	5.148	
1250	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Subtracted	218.368	213.22	5.148	
1250	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [source:swissprot;acc:p48059]	Divided	219.354	224.7	1.02437	
1251	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [source:swissprot;acc:q13418]	Divided	219.354	224.7	1.02437	
1251	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	Subtracted	218.368	213.22	5.148	
1252	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	Subtracted	218.368	213.22	5.148	
1252	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]	Divided	219.354	224.7	1.02437	
1253	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Subtracted	218.368	213.22	5.148	
1253	ras suppressor protein 1 (rsu-1) (rsp-1). [source:swissprot;acc:q15404]	Divided	219.354	224.7	1.02437	
1254	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	Subtracted	218.368	213.22	5.148	
1254	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [source:swissprot;acc:q13283]	Divided	219.354	224.7	1.02437	
1255	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [source:sptrembl;acc:q9ntl5]	Subtracted	218.368	213.22	5.148	
1255	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [source:swissprot;acc:q9un86]	Divided	219.354	224.7	1.02437	
1256	cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [source:swissprot;acc:p13584]	Subtracted	218.368	213.22	5.148	
1256	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	Divided	219.354	224.699	1.02437	
1257	espin. [source:refseq;acc:nm_031475]	Divided	219.354	224.7	1.02437	
1257	flotillin-1. [source:swissprot;acc:o75955]	Subtracted	218.368	213.22	5.148	
1258	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [source:swissprot;acc:p10635]	Divided	219.354	224.7	1.02437	
1258	sestrin 1 (p53-regulated protein pa26). [source:swissprot;acc:q9y6p5]	Subtracted	218.368	213.22	5.148	
1259	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [source:refseq;acc:nm_006832]	Divided	219.354	224.7	1.02437	
1259	signal transducer and activator of transcription 5a. [source:swissprot;acc:p42229]	Subtracted	222.546	227.673	5.127	
1260	lim and senescent cell antigen-like domains 2; ilk-binding protein. [source:refseq;acc:nm_017980]	Divided	219.354	224.7	1.02437	
1260	signal transducer and activator of transcription 5b. [source:swissprot;acc:p51692]	Subtracted	222.544	227.667	5.123	
1261	d(4) dopamine receptor (d(2c) dopamine receptor). [source:swissprot;acc:p21917]	Divided	219.354	224.7	1.02437	
1261	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	Subtracted	163.24	168.359	5.119	
1262	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	Divided	219.353	224.678	1.02428	
1262	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [source:swissprot;acc:q9unq2]	Subtracted	226.347	221.259	5.088	
1263	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]	Divided	171.231	167.177	1.02425	
1263	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Subtracted	212.724	207.637	5.087	

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/