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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 768 to 817 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
384	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	244.236	266.421	1.09083
385	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Subtracted	208.756	227.575	18.819
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Divided	244.236	266.421	1.09083
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]		264.11	242.238	1.09029
	40s ribosomal protein s9. [swissprot;acc:p46781]	Subtracted	257.784	238.986	18.798
387	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Divided	264.11	242.238	1.09029
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Subtracted	75.3531	56.6768	18.6763
388	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		75.3948	56.7244	18.6704
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Divided	208.756	227.575	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	75.3954	56.7252	18.6702
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Divided	208.756	227.575	1.09015
390	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]		263.62	241.828	1.09011
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Subtracted	75.447	56.7841	18.6629
391	40s ribosomal protein s16. [swissprot;acc:p17008]	Divided	263.62	241.828	1.09011
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Subtracted	207.072	225.719	18.647
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	Divided	263.615	241.83	1.09008
	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	Subtracted	257.705	239.092	18.613
393	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]		257.327	238.921	18.406
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Divided	207.072	225.719	1.09005
394	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	Subtracted	226.226	207.889	18.337
	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Divided	238.407	218.827	1.08948
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
	phosducin-like protein (phlp). [swissprot;acc:q13371]	Subtracted	226.218	207.908	18.31
396	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Divided	262.34	240.801	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	226.218	207.908	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	101.613	110.689	1.08932
398	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]		238.358	218.818	1.0893
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Subtracted	226.218	207.908	18.31
399	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	Divided	226.226	207.889	1.08821
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Subtracted	226.218	207.908	18.31
400	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]		226.209	207.931	18.278
	phosducin-like protein (phlp). [swissprot;acc:q13371]	Divided	226.218	207.908	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	236.224	254.434	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	226.218	207.908	1.08807
402	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Subtracted	249.983	231.802	18.181
	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Divided	226.218	207.908	1.08807
403	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Subtracted	246.338	228.468	17.87
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Divided	226.218	207.908	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	246.33	228.463	17.867
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Divided	226.218	207.908	1.08807
405	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]		226.209	207.931	1.0879
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Subtracted	83.0461	65.4586	17.5875
406	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		254.667	237.109	17.558
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Divided	244.304	265.634	1.08731
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		260.544	239.75	1.08673
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Subtracted	254.667	237.109	17.558
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Divided	234.804	255.112	1.08649
	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	Subtracted	254.667	237.109	17.558
409	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Divided	261.874	241.045	1.08641

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.