MK5 Microarray Data

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.

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

Results: HTML CSV LaTeX

Showing element 436 to 485 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	red	green	network_comparison
436	PXN	paxillin. [swissprot;acc:p49023]	221.522	205.286	1.07909
437	TRIP10	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	209.921	226.459	1.07878
438	ARD1A	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	233.723	216.674	1.07869
439	RPS9	40s ribosomal protein s9. [swissprot;acc:p46781]	238.986	257.784	1.07866
440	NDC80	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	231.802	249.983	1.07843
441	GRAP	grb2-related adaptor protein. [swissprot;acc:q13588]	223.457	207.222	1.07835
442	ANKS1B	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	223.802	207.55	1.0783
443	NAV2	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	223.79	207.539
444	NAV1	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	223.801	207.549
445	NAV3	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]
446	GRB2	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	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). [swissprot;acc:p51955]
448	MACF1	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	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). [swissprot;acc:q03001]	228.463	246.33	1.07821
450	SRP9	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	235.94	218.837	1.07815
451	POLR3C	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	239.092	257.705	1.07785
452	no value	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	224.161	207.972	1.07784
453	SNRPA1	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
454	no value	40s ribosomal protein s26. [swissprot;acc:p02383]	210.224	226.578	1.07779
455	TIMM22	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	210.225
456	ATPAF2	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
457	UQCRB	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]
458	SRP9	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	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). [swissprot;acc:o95817]	233.529	216.737	1.07748
460	SF3A2	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	223.648	207.62	1.0772
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). [swissprot;acc:q13887]
462	MKI67IP	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	254.434	236.224	1.07709
463	POLR3F	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	238.921	257.327	1.07704
464	FNBP1	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	210.578	226.764	1.07686
465	CHRNA7	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	248.152	267.226
466	ADCY6	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
467	ADCY5	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]
468	LRRC15	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]
469	FEM1B	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
470	LRRC3	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]
471	LAMC1	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]
472	SLC46A2	thymic stromal co-transporter. [refseq;acc:nm_033051]
473	PRPF31	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	225.661	209.651	1.07637
474	KCNA2	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	226.789	210.818	1.07576
475	KCNA1	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	226.727	210.816	1.07547
476	KCNA4	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	226.681	210.814	1.07527
477	NIP7	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	251.926	234.547	1.0741
478	BRF1	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). [swissprot;acc:q92994]	228.051	212.321	1.07409
479	NOLA1	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
480	NETO2	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	237.109	254.667	1.07405
481	NETO1	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]
482	HNRNPU	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]
483	RUNX2	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]
484	HNRPUL1	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
485	RPL18	60s ribosomal protein l18. [swissprot;acc:q07020]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.