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.


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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1032 to 1081 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Value Type	description	red	green	network_comparison	
258	Rooted	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	51.6132	45.8422	1.12589	
259	Measured	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	6417.81	7852.52	1.22355	
259	Ranked	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	227.999	204.37	1.11562	
259	Squared	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4]	76360.8	58841.7	1.29773	
259	Rooted	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	58.2964	65.5926	1.12516	
260	Measured	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	4244.95	5193.42	1.22343	
260	Ranked	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	219.421	196.978	1.11394	
260	Squared	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	76296.4	58801.6	1.29752	
260	Rooted	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	59.0951	66.4332	1.12417	
261	Measured	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	4247.36	5192.61	1.22255	
261	Ranked	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	219.421	196.978	1.11394	
261	Squared	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	48127.9	62245.6	1.29334	
261	Rooted	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	62.3337	70.0738	1.12417	
262	Measured	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	24896.4	20431.7	1.21852	
262	Ranked	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	219.421	196.978	1.11394	
262	Squared	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	26157.6	20236.2	1.29261	
262	Rooted	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	59.4073	66.7002	1.12276	
263	Measured	trs85 homolog. [source:swissprot;acc:q9y2l5]	24896.4	20431.7	1.21852	
263	Ranked	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	219.421	196.978	1.11394	
263	Squared	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	26157.6	20236.2	1.29261	
263	Rooted	paxillin. [source:swissprot;acc:p49023]	59.4073	66.7002	1.12276	
264	Measured	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	4987.58	4094.57	1.2181	
264	Ranked	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	219.421	196.978	1.11394	
264	Squared	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	26157.6	20236.2	1.29261	
264	Rooted	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	66.1122	74.1438	1.12148	
265	Measured	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	24806.9	20369.9	1.21782	
265	Ranked	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	225.217	202.459	1.11241	
265	Squared	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	26157.6	20236.2	1.29261	
265	Rooted	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	56.031	62.8281	1.12131	
266	Measured	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	24806.9	20369.9	1.21782	
266	Ranked	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	241.07	267.88	1.11121	
266	Squared	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	26157.6	20236.2	1.29261	
266	Rooted	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	66.1064	74.1074	1.12103	
267	Measured	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	14021.4	11523	1.21682	
267	Ranked	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	241.07	267.88	1.11121	
267	Squared	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	26157.6	20236.2	1.29261	
267	Rooted	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	66.1064	74.1073	1.12103	
268	Measured	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	24473.9	20127.8	1.21593	
268	Ranked	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	271.016	244.167	1.10996	
268	Squared	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	26157.6	20236.2	1.29261	
268	Rooted	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	66.1064	74.1074	1.12103	
269	Measured	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	4590.18	5575.52	1.21466	
269	Ranked	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	241.373	267.352	1.10763	
269	Squared	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	26157.6	20236.2	1.29261	
269	Rooted	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	66.1064	74.1074	1.12103	
270	Measured	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	23640.2	19479.8	1.21358	
270	Ranked	fad synthetase. [source:refseq;acc:nm_025207]	241.373	267.352	1.10763	
270	Squared	transcription factor iib. [source:refseq;acc:nm_013242]	64739.9	50300.6	1.28706	
270	Rooted	crk-like protein. [source:swissprot;acc:p46109]	66.1064	74.1074	1.12103	
271	Measured	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	2554.89	3093.78	1.21092	

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/