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 763 to 812 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
382	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	Subtracted	253.852	234.808	19.044
	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Divided	200.791	183.66	1.09328
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]		237.862	217.739	1.09242
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Subtracted	236.245	255.113	18.868
384	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]		227.575	208.756	18.819
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Divided	266.421	244.236	1.09083
385	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Subtracted	227.575	208.756	18.819
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Divided	266.421	244.236	1.09083
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]		242.238	264.11	1.09029
	40s ribosomal protein s9. [swissprot;acc:p46781]	Subtracted	238.986	257.784	18.798
387	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Divided	242.238	264.11	1.09029
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Subtracted	56.6768	75.3531	18.6763
388	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		56.7244	75.3948	18.6704
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Divided	227.575	208.756	1.09015
389	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Subtracted	56.7252	75.3954	18.6702
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Divided	227.575	208.756	1.09015
390	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]		241.828	263.62	1.09011
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Subtracted	56.7841	75.447	18.6629
391	40s ribosomal protein s16. [swissprot;acc:p17008]	Divided	241.828	263.62	1.09011
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Subtracted	225.719	207.072	18.647
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	Divided	241.83	263.615	1.09008
	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	Subtracted	239.092	257.705	18.613
393	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	18.406
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Divided	225.719	207.072	1.09005
394	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	Subtracted	207.889	226.226	18.337
	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Divided	218.827	238.407	1.08948
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
	phosducin-like protein (phlp). [swissprot;acc:q13371]	Subtracted	207.908	226.218	18.31
396	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Divided	240.801	262.34	1.08945
	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	Subtracted	207.908	226.218	18.31
397	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	Divided	110.689	101.613	1.08932
398	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]		218.818	238.358	1.0893
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Subtracted	207.908	226.218	18.31
399	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	Divided	207.889	226.226	1.08821
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Subtracted	207.908	226.218	18.31
400	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]		207.931	226.209	18.278
	phosducin-like protein (phlp). [swissprot;acc:q13371]	Divided	207.908	226.218	1.08807
401	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Subtracted	254.434	236.224	18.21
	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	Divided	207.908	226.218	1.08807
402	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Subtracted	231.802	249.983	18.181
	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Divided	207.908	226.218	1.08807
403	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Subtracted	228.468	246.338	17.87
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Divided	207.908	226.218	1.08807
404	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]	Subtracted	228.463	246.33	17.867
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Divided	207.908	226.218	1.08807
405	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]		207.931	226.209	1.0879
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Subtracted	65.4586	83.0461	17.5875
406	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		237.109	254.667	17.558
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Divided	265.634	244.304	1.08731

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.