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.

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 713 to 762 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	1	243.12	266.661	1.09683
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	0	16321	15577	1.04776
358	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	1	243.12	266.662	1.09683
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]		239.277	262.434	1.09678
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	0	16321	15577	1.04776
360	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	1	243.072	266.559	1.09663
361	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	0	16321	15577	1.04776
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	1	242.83	266.248	1.09644
362	apical-like protein (apxl protein). [swissprot;acc:q13796]		231.492	211.136	1.09641
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	0	16321	15577	1.04776
363	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	1	231.481	211.131	1.09639
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]		243.208	266.617	1.09625
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	0	16321	15577	1.04776
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	1	242.744	266.07	1.09609
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	0	7769.96	8139.71	1.04759
366	40s ribosomal protein s5. [swissprot;acc:p46782]	1	242.473	265.756	1.09602
	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	0	8614.89	9017.27	1.04671
367	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]		13801.7	13185.9	1.0467
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	1	234.146	256.627	1.09601
368	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	0	16679.2	15940.6	1.04633
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	1	242.66	265.715	1.09501
369	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	0	18849.7	19704.7	1.04536
	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	1	242.159	265.104	1.09475
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	0	13652.7	13061	1.0453
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	1	186.52	170.42	1.09447
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	0	13247.9	12674.2	1.04527
372	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]		11869.9	12402.7	1.04489
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	1	186.52	170.42	1.09447
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]		242.37	265.255	1.09442
	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	0	10598.2	11061.5	1.04371
374	calcyphosine. [swissprot;acc:q13938]		9874.54	9478.1	1.04183
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	1	267.208	244.168	1.09436
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]		242.686	265.516	1.09407
	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	0	14247.6	13686.9	1.04097
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	1	257.017	234.945	1.09395
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	0	10284.9	10695.6	1.03993
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	1	242.691	265.481	1.09391
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	0	14512.3	13958.2	1.0397
378	60s ribosomal protein l30. [swissprot;acc:p04645]	1	242.593	265.365	1.09387
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	0	19713.5	18962.5	1.0396
379	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]		11228.4	10806	1.03909
	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	1	241.509	264.163	1.0938
380	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	0	9566.15	9936.37	1.0387
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	1	242.109	264.79	1.09368
381	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	0	9565.54	9935.19	1.03864
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	1	200.586	183.423	1.09357

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.