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

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Showing element 1001 to 1050 of 3730 in total

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

description	Rank	Filtered	red	green	network_comparison
dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889]	2801	1	0.00001	0.00001	1
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	950		252.873	261.821	1.03539
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542]	1702		216.079	219.024	1.01363
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]	771		210.946	221.225	1.04873
dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]	575		221.807	208.264	1.06503
dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]	768		210.946	221.225	1.04873
dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]	770
doc-1 related protein (doc-1r). [swissprot;acc:o75956]	331		312	284	1.09859
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	655		216.504	204.622	1.05807
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	654
dok-like protein. [refseq;acc:nm_024872]	92	0	17571	21783	1.23971
	653	1	216.504	204.622	1.05807
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	991		203.381	196.76	1.03365
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	257		200.691	179.88	1.11569
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	1020		221.28	214.409	1.03205
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]	1046		173.475	178.889	1.03121
double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]	3054		0.00001	0.00001	1
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	2725		216.496	216.569	1.00034
doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240]	3187		0.00001	0.00001	1
down-regulated in metastasis. [refseq;acc:nm_014503]	787		244.447	233.508	1.04685
dpy-30-like protein. [swissprot;acc:q9c005]	1815		220.462	217.926	1.01164
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	1468		212.001	207.937	1.01954
dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	2069		217.555	215.807	1.0081
dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]	2072
dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734]	2385		210.595	209.767	1.00395
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	2326		220.076	219.05	1.00468
dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564]	2384		210.57	209.737	1.00397
dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733]	2139		221.248	222.788	1.00696
dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319]	2926		0.00001	0.00001	1
dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627]	1800		217.011	214.481	1.0118
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463]	1803
dymeclin. [refseq;acc:nm_017653]	2055		218.79	216.981	1.00834
dynactin 4. [refseq;acc:nm_032486]	426		233.142	252.253	1.08197
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	1549		225.159	221.424	1.01687
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]	2081		215.967	214.28	1.00787
dynein 2 light intermediate chain. [refseq;acc:nm_016008]	2962		0.00001	0.00001	1
dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [swissprot;acc:q9ui46]	3029
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	1005		225.448	218.232	1.03307
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	998		225.557	218.271	1.03338
dynein light chain 2. [refseq;acc:nm_080677]	647		216.731	229.549	1.05914
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	286	0	12228.2	11367.3	1.07573
	1085	1	231.007	237.864	1.02968
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	2583		213.415	213.743	1.00154
dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	2581		213.428	213.756
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	26	0	12128.3	7533.33	1.60995
	1599	1	217.871	214.404	1.01617
dystrophin. [swissprot;acc:p11532]	14	0	10232.5	18054.8	1.76446
	2584	1	213.422	213.75	1.00154
e-1 enzyme. [refseq;acc:nm_021204]	2251		208.315	207.061	1.00606
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	65	0	7853.67	10406.3	1.32502

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.