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

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Showing element 680 to 729 of 3228 in total

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

Rank	description	red	green	network_comparison
680	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	6503.03	7282.5	1.11986
681	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	7170.83	8029.64	1.11976
682	syntaxin 12. [refseq;acc:nm_177424]	5552.92	6217.59	1.1197
683	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	7139.5	7994.06	1.11969
684	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	4359.82	4880.99	1.11954
685	metaxin 1. [swissprot;acc:q13505]	9327.58	10442.2	1.1195
686	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	6920.69	7747.63	1.11949
687	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	6920.71	7747.65
688	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	6920.67	7747.6
689	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	6920.69	7747.63
690	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]
691	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]
692	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
693	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	7725.1	8647.74	1.11943
694	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
695	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]
696	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
697	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	7105.27	7953.71	1.11941
698	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	7101.95	7949.85	1.11939
699	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	7101.94	7949.84
700	40s ribosomal protein s28. [swissprot;acc:p25112]	7161.14	8015.92	1.11936
701	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	7802.31	8731.82	1.11913
702	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	7067.46	7909.27	1.11911
703	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	6912.56	7735.12	1.11899
704	alpha-nac protein. [sptrembl;acc:q9h009]	6912.27	7734.68	1.11898
705	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	6912.09	7734.41	1.11897
706	di-ras2. [refseq;acc:nm_017594]	6912.08	7734.39
707	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	5317.78	5944.25	1.11781
708	z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]
709	pp1201 protein. [refseq;acc:nm_022152]
710	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
711	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]
712	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]
713	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	3996.81	4465.61	1.11729
714	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	5222.71	5834.57	1.11715
715	dendritic cell protein. [refseq;acc:nm_006360]	6593.17	7364.55	1.117
716	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]
717	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
718	cpz gene product. [refseq;acc:nm_003652]
719	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
720	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]
721	syntaxin 7. [swissprot;acc:o15400]	5580.97	6233.52	1.11692
722	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	8061.05	9002.33	1.11677
723	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	8056.09	8996.46	1.11673
724	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	5384.41	6012.82	1.11671
725	phenylalanine-trna synthetase. [refseq;acc:nm_006567]
726	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	6327.86	7064.13	1.11635
727	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	7087.23	7911.25	1.11627
728	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	6000.23	6696.89	1.11611
729	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]

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
- 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.