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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 880 to 929 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
440	NDC80	highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	Divided	231.802	249.983	1.07843	
441	GRAP	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Divided	223.457	207.222	1.07835	
441	TIMM22	mitochondrial import inner membrane translocase subunit tim22. [source:swissprot;acc:q9y584]	Subtracted	210.225	226.578	16.353	
442	ANKS1B	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Divided	223.802	207.55	1.0783	
442	ATPAF2	atp synthase mitochondrial f1 complex assembly factor 2. [source:refseq;acc:nm_145691]	Subtracted	210.225	226.578	16.353	
443	NAV2	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	Divided	223.79	207.539	1.0783	
443	UQCRB	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [source:swissprot;acc:p14927]	Subtracted	210.225	226.578	16.353	
444	NAV1	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Divided	223.801	207.549	1.0783	
444	NOL1	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	Subtracted	250.053	233.725	16.328	
445	GNL3	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	Subtracted	250.858	234.563	16.295	
445	NAV3	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Divided	223.801	207.549	1.0783	
446	GRB2	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354]	Divided	224.049	207.785	1.07827	
446	GRB2	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354]	Subtracted	224.049	207.785	16.264	
447	NEK2	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955]	Divided	224.049	207.785	1.07827	
447	NEK2	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955]	Subtracted	224.049	207.785	16.264	
448	ANKS1B	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Subtracted	223.802	207.55	16.252	
448	MACF1	microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2]	Divided	228.468	246.338	1.07822	
449	DST	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [source:swissprot;acc:q03001]	Divided	228.463	246.33	1.07821	
449	NAV1	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Subtracted	223.801	207.549	16.252	
450	NAV3	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Subtracted	223.801	207.549	16.252	
450	SRP9	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Divided	235.94	218.837	1.07815	
451	NAV2	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	Subtracted	223.79	207.539	16.251	
451	POLR3C	polymerase (rna) iii (dna directed) (62kd). [source:refseq;acc:nm_006468]	Divided	239.092	257.705	1.07785	
452		ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Divided	224.161	207.972	1.07784	
452	POLI	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Subtracted	221.522	205.286	16.236	
453	PXN	paxillin. [source:swissprot;acc:p49023]	Subtracted	221.522	205.286	16.236	
453	SNRPA1	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Divided	224.161	207.972	1.07784	
454		40s ribosomal protein s26. [source:swissprot;acc:p02383]	Divided	210.224	226.578	1.07779	
454	GRAP	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Subtracted	223.457	207.222	16.235	
455		ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Subtracted	224.161	207.972	16.189	
455	TIMM22	mitochondrial import inner membrane translocase subunit tim22. [source:swissprot;acc:q9y584]	Divided	210.225	226.578	1.07779	
456	ATPAF2	atp synthase mitochondrial f1 complex assembly factor 2. [source:refseq;acc:nm_145691]	Divided	210.225	226.578	1.07779	
456	SNRPA1	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Subtracted	224.161	207.972	16.189	
457	FNBP1	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6]	Subtracted	210.578	226.764	16.186	
457	UQCRB	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [source:swissprot;acc:p14927]	Divided	210.225	226.578	1.07779	
458	DDX18	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	Subtracted	251.653	235.506	16.147	
458	SRP9	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Divided	235.922	218.925	1.07764	
459	BAG3	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	Divided	233.529	216.737	1.07748	
459	RRP1	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	Subtracted	250.538	234.401	16.137	
460	RPS6KC1	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Subtracted	186.52	170.42	16.1	
460	SF3A2	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Divided	223.648	207.62	1.0772	
461		ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Subtracted	186.52	170.42	16.1	
461	KLF5	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Divided	223.648	207.62	1.0772	
462	MKI67IP	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	Divided	254.434	236.224	1.07709	
462	POLR2H	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	Subtracted	236.662	252.708	16.046	
463	POLR3F	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9]	Divided	238.921	257.327	1.07704	
463	SF3A2	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Subtracted	223.648	207.62	16.028	
464	FNBP1	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6]	Divided	210.578	226.764	1.07686	
464	KLF5	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Subtracted	223.648	207.62	16.028	
465	CHRNA7	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Divided	248.152	267.226	1.07686	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/