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 2858 to 2907 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
715	dendritic cell protein. [source:refseq;acc:nm_006360]	Measured	6593.17	7364.55	1.117	
715	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [source:refseq;acc:nm_139279]	Rooted	61.0097	65.3071	1.07044	
715	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Squared	25911.5	30281.9	1.16867	
716	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	Squared	25911.5	30281.9	1.16867	
716	cpz gene product. [source:refseq;acc:nm_003652]	Ranked	223.121	211.685	1.05402	
716	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	Rooted	61.0098	65.3071	1.07044	
716	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	Measured	6593.17	7364.55	1.117	
717	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	Ranked	223.121	211.685	1.05402	
717	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	Measured	6593.17	7364.55	1.117	
717	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	Rooted	61.0111	65.3081	1.07043	
717	sec13-related protein. [source:swissprot;acc:p55735]	Squared	25911.7	30282.1	1.16867	
718	cpz gene product. [source:refseq;acc:nm_003652]	Measured	6593.17	7364.55	1.117	
718	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	Rooted	60.7498	65.0218	1.07032	
718	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [source:swissprot;acc:q96sm3]	Ranked	223.121	211.685	1.05402	
718	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [source:swissprot;acc:q96lb4]	Squared	25911.5	30281.9	1.16867	
719	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	Measured	6593.17	7364.55	1.117	
719	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	Ranked	247.769	235.074	1.054	
719	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	Rooted	60.7498	65.0218	1.07032	
719	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Squared	25911.7	30282.1	1.16867	
720	60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	Ranked	231.92	244.435	1.05396	
720	jm1 protein. [source:refseq;acc:nm_014008]	Rooted	61.5849	65.9155	1.07032	
720	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [source:swissprot;acc:q96sm3]	Measured	6593.17	7364.55	1.117	
720	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [source:swissprot;acc:o75348]	Squared	25911.5	30281.9	1.16867	
721	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	Ranked	214.765	203.8	1.0538	
721	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [source:refseq;acc:nm_139126]	Rooted	60.8463	65.123	1.07029	
721	syntaxin 7. [source:swissprot;acc:o15400]	Measured	5580.97	6233.52	1.11692	
721	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [source:swissprot;acc:p36543]	Squared	25911.7	30282.1	1.16867	
722	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Rooted	58.4551	62.5601	1.07022	
722	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	Squared	25911.7	30282.1	1.16867	
722	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	Measured	8061.05	9002.33	1.11677	
722	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [source:swissprot;acc:o43280]	Ranked	217.952	206.902	1.05341	
723	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [source:refseq;acc:nm_005804]	Squared	25911.5	30281.9	1.16867	
723	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	Rooted	51.7007	48.3103	1.07018	
723	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Measured	8056.09	8996.46	1.11673	
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	Ranked	244.842	232.577	1.05274	
724	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Ranked	244.842	232.577	1.05274	
724	ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	Squared	25911.7	30282.1	1.16867	
724	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	Measured	5384.41	6012.82	1.11671	
724	syntaxin 12. [source:refseq;acc:nm_177424]	Rooted	61.3557	65.66	1.07015	
725	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	Rooted	57.5045	53.7387	1.07008	
725	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	Ranked	235.296	247.673	1.0526	
725	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	Measured	5384.41	6012.82	1.11671	
725	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [source:swissprot;acc:q9y5k8]	Squared	25911.7	30282.1	1.16867	
726	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	Measured	6327.86	7064.13	1.11635	
726	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Ranked	244.495	232.419	1.05196	
726	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	Squared	25911.7	30282.1	1.16867	
726	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	Rooted	51.4482	55.0529	1.07006	
727	60s ribosomal protein l24 (l30). [source:swissprot;acc:p38663]	Measured	7087.23	7911.25	1.11627	
727	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [source:swissprot;acc:o60285]	Ranked	208.873	219.71	1.05188	
727	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	Rooted	59.7414	63.909	1.06976	

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/