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 677 to 726 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	red	green	network_comparison	
677	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	228.944	216.745	1.05628	
678	sorting nexin 5. [source:swissprot;acc:q9y5x3]	208.482	220.175	1.05609	
679	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	132.413	125.389	1.05602	
680	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	132.413	125.389	1.05602	
681	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	132.413	125.389	1.05602	
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	132.413	125.389	1.05602	
683	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	132.413	125.389	1.05602	
684	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	132.413	125.389	1.05602	
685	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	132.413	125.389	1.05602	
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	132.413	125.389	1.05602	
687	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	132.413	125.389	1.05602	
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	237.554	250.823	1.05586	
689	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	135.379	128.225	1.05579	
690	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	220.593	208.987	1.05553	
691	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm_005872]	217.602	206.195	1.05532	
692	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [source:refseq;acc:nm_001253]	217.602	206.195	1.05532	
693	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]	222.554	234.847	1.05524	
694	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [source:swissprot;acc:q07864]	241.907	229.35	1.05475	
695	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]	226.135	214.405	1.05471	
696	sr rich protein. [source:refseq;acc:nm_032870]	225.293	213.64	1.05455	
697	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	220.444	209.113	1.05419	
698	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	220.437	209.118	1.05413	
699	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	220.438	209.118	1.05413	
700	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	220.438	209.118	1.05413	
701	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	220.438	209.118	1.05413	
702	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	220.438	209.118	1.05413	
703	limkain b1. [source:refseq;acc:nm_019081]	220.438	209.118	1.05413	
704	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	220.438	209.118	1.05413	
705	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	220.438	209.118	1.05413	
706	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	220.438	209.118	1.05413	
707	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	220.438	209.118	1.05413	
708	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	220.438	209.118	1.05413	
709	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	220.438	209.118	1.05413	
710	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	220.438	209.118	1.05413	
711	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [source:swissprot;acc:p54577]	232.468	245.048	1.05411	
712	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	220.431	209.123	1.05407	
713	dendritic cell protein. [source:refseq;acc:nm_006360]	223.121	211.685	1.05402	
714	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	223.121	211.685	1.05402	
715	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]	223.121	211.685	1.05402	
716	cpz gene product. [source:refseq;acc:nm_003652]	223.121	211.685	1.05402	
717	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	223.121	211.685	1.05402	
718	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [source:swissprot;acc:q96sm3]	223.121	211.685	1.05402	
719	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	247.769	235.074	1.054	
720	60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	231.92	244.435	1.05396	
721	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	214.765	203.8	1.0538	
722	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [source:swissprot;acc:o43280]	217.952	206.902	1.05341	
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	244.842	232.577	1.05274	
724	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	244.842	232.577	1.05274	
725	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	235.296	247.673	1.0526	
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]	244.495	232.419	1.05196	

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/