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	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 775 to 824 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
388	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Subtracted	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
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		239.75	260.544	1.08673
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Subtracted	237.109	254.667	17.558
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Divided	255.112	234.804	1.08649
	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	Subtracted	237.109	254.667	17.558
409	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Divided	241.045	261.874	1.08641
	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]	Subtracted	237.109	254.667	17.558
410	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Divided	233.376	253.539	1.0864
411	60s ribosomal protein l18. [swissprot;acc:q07020]	Subtracted	237.109	254.667	17.558
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Divided	233.376	253.539	1.0864
412	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Subtracted	251.926	234.547	17.379
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Divided	240.788	261.416	1.08567

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.