Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5908 to 5957 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1477 transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Ranked 215.328 211.267 1.01922
1478 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 215.122 211.066
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Measured 5659.22 6084.68 1.07518
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Rooted 65.7121 68.2158 1.0381
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] Squared 26860.7 29969 1.11572
1479 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Measured 5787.03 6221.72 1.07511
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Rooted 65.7121 68.2158 1.0381
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Ranked 228.469 232.855 1.0192
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Squared 26860.7 29969 1.11572
1480 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] Ranked 218.664 214.55 1.01918
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Measured 5660.17 6085.22 1.07509
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Squared 15124.2 16872.9 1.11562
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Rooted 65.7121 68.2158 1.0381
1481 26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] Squared 26142.6 29163.8 1.11557
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Ranked 208.432 204.516 1.01915
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Measured 3688.8 3431.33 1.07504
mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Rooted 63.582 66.002 1.03806
1482 enigma protein; lim domain protein. [refseq;acc:nm_005451] 61.1844 63.5127 1.03805
leng5 protein. [refseq;acc:nm_024075] Measured 5372.25 5775.21 1.07501
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Ranked 224.354 220.15 1.0191
protein bap28. [swissprot;acc:q9h583] Squared 14997.9 16728.4 1.11538
1483 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 31810.3 35473.9 1.11517
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Rooted 61.1844 63.5127 1.03805
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Ranked 198.927 202.726 1.0191
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Measured 5372.25 5775.21 1.07501
1484 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] Ranked 198.927 202.726 1.0191
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Squared 22974.7 25619.9 1.11514
evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] Rooted 64.2463 66.6861 1.03798
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Measured 5372.25 5775.21 1.07501
1485 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Squared 26696.5 29768.6 1.11508
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Ranked 207.877 203.989 1.01906
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Rooted 59.2072 61.4511 1.0379
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Measured 5372.25 5775.21 1.07501
1486 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Rooted 79.3006 82.3013 1.03784
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Ranked 207.877 203.989 1.01906
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Squared 26696.5 29768.6 1.11508
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Measured 5372.25 5775.21 1.07501
1487 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Squared 26696.5 29768.6 1.11508
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] Rooted 62.3212 64.678 1.03782
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Measured 5573.64 5991.58 1.07499
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Ranked 207.877 203.989 1.01906
1488 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Measured 5573.64 5991.58 1.07499
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Ranked 207.877 203.989 1.01906
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Squared 26696.5 29768.6 1.11508
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Rooted 62.3212 64.678 1.03782
1489 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Squared 26277.3 29299.3 1.115
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] Rooted 62.3212 64.678 1.03782
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Ranked 213.251 209.264 1.01905
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Measured 6192.38 6656.34 1.07492
1490 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 6340.5 6815.41 1.0749

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.
- http://analysis.yellowcouch.org/