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 1963 to 2012 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
246	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Rooted	Subtracted	27.9136	37.2872	9.3736	
246	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Ranked	Divided	237.312	212.363	1.11748	
246	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Squared	Divided	8875.01	6768.05	1.31131	
246	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	Squared	Subtracted	54726.7	45358.5	9368.2	
246	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Measured	Divided	4252.66	5213.05	1.22583	
246	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Rooted	Divided	146.94	167.046	1.13683	
247	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Ranked	Subtracted	243.583	267.527	23.944	
247	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Measured	Subtracted	13241.4	11864	1377.4	
247	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Squared	Divided	8875.01	6768.05	1.31131	
247	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Rooted	Subtracted	27.9136	37.2872	9.3736	
247	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Squared	Subtracted	33982.3	43159.1	9176.8	
247	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Rooted	Divided	47.3621	53.8355	1.13668	
247	rna-binding protein. [source:refseq;acc:nm_019027]	Ranked	Divided	237.302	212.41	1.11719	
247	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Measured	Divided	6416.68	7865.15	1.22574	
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Ranked	Divided	237.302	212.41	1.11719	
248	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	Ranked	Subtracted	243.583	267.527	23.944	
248	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [source:swissprot;acc:p48735]	Squared	Subtracted	37226.9	46400.1	9173.2	
248	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Squared	Divided	8875.01	6768.05	1.31131	
248	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Rooted	Subtracted	27.9136	37.2872	9.3736	
248	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Measured	Subtracted	13241.4	11864	1377.4	
248	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Measured	Divided	6417.18	7859.6	1.22477	
248	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Rooted	Divided	56.0466	63.4808	1.13264	
249	cell division cycle protein 23; anaphase-promoting complex subunit 8. [source:refseq;acc:nm_004661]	Squared	Subtracted	51616.7	42588.9	9027.8	
249	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Squared	Divided	8875.01	6768.05	1.31131	
249	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Rooted	Subtracted	27.9136	37.2872	9.3736	
249	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Ranked	Divided	237.302	212.41	1.11719	
249	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Measured	Subtracted	4405.4	5782.08	1376.68	
249	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Ranked	Subtracted	226.109	202.333	23.776	
249	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Rooted	Divided	55.5965	62.9349	1.13199	
249	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Measured	Divided	6417.18	7859.59	1.22477	
250	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	Squared	Divided	69201.8	53013.4	1.30536	
250	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Rooted	Subtracted	27.9136	37.2872	9.3736	
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Ranked	Divided	237.302	212.41	1.11719	
250	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	Squared	Subtracted	34527.9	43507.9	8980	
250	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Rooted	Divided	55.5965	62.9349	1.13199	
250	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Ranked	Subtracted	210.693	186.95	23.743	
250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Measured	Divided	6417.18	7859.6	1.22477	
250	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]	Measured	Subtracted	4578.09	5939.91	1361.82	
251	40s ribosomal protein s20. [source:swissprot;acc:p17075]	Ranked	Subtracted	243.5	267.21	23.71	
251	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	Squared	Divided	69165.6	52992.1	1.30521	
251	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Measured	Subtracted	4579.34	5940.64	1361.3	
251	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Rooted	Subtracted	27.9136	37.2872	9.3736	
251	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Squared	Subtracted	34506.3	43476	8969.7	
251	max protein. [source:swissprot;acc:p25912]	Rooted	Divided	56.3054	63.7148	1.13159	
251	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Ranked	Divided	186.172	166.661	1.11707	
251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Measured	Divided	6417.18	7859.6	1.22477	
252	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	Squared	Subtracted	51286.6	42334.5	8952.1	
252	crk-like protein. [source:swissprot;acc:p46109]	Measured	Divided	6417.18	7859.6	1.22477	
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Ranked	Divided	237.292	212.457	1.11689	
252	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	Measured	Subtracted	9648.27	10994.9	1346.63	

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/