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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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5930 to 5979 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
1483 NCK2 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Squared 31810.3 35473.9 1.11517
PDHB 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
WARS 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 no value ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Squared 22974.7 25619.9 1.11514
ECSIT evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] Rooted 64.2463 66.6861 1.03798
TMEM91 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
1485 C11orf2 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Squared 26696.5 29768.6 1.11508
MTFMT methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Rooted 59.2072 61.4511 1.0379
RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Ranked 207.877 203.989 1.01906
WARS2 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 no value thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Rooted 79.3006 82.3013 1.03784
HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Ranked 207.877 203.989 1.01906
KIF13A kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Squared 26696.5 29768.6 1.11508
1487 COG2 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]
HIVEP1 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
MAP2K1 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
NMNAT3 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Measured 5573.64 5991.58 1.07499
1488 no value kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Squared 26696.5 29768.6 1.11508
ALDH18A1 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
HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Ranked 207.877 203.989 1.01906
KSR1 similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Rooted 62.3212 64.678 1.03782
1489 MAP2K2 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]
MAP3K7 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
NSF 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
PSMC4 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
1490 CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Measured 6340.5 6815.41 1.0749
CCT5 t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Rooted 81.8175 78.8388 1.03778
ING5 p28 ing5. [refseq;acc:nm_032329] Squared 26142 29139.6 1.11467
PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] Ranked 221.961 226.186 1.01903
1491 CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Rooted 100.828 97.1592 1.03776
FIGNL1 fidgetin-like 1. [refseq;acc:nm_022116] Measured 6057.46 6510.9 1.07486
GPI glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Ranked 217.704 221.839 1.01899
LOH12CR1 loh1cr12. [refseq;acc:nm_058169] Squared 23620.8 26329.4 1.11467
1492 CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Rooted 64.4465 66.8769 1.03771
CSDE1 unr protein. [swissprot;acc:o75534] Squared 23620.8 26329.4 1.11467
MCM3 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Measured 4619.81 4965.45 1.07482
OPCML opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Ranked 224.159 220.017 1.01883
1493 C16orf42 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Rooted 66.7295 69.2425 1.03766
DHPS deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] Measured 6146.36 6606.21 1.07482
PDHA2 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Ranked 204.146 207.988 1.01882
POLE3 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Squared 12403.8 13821.4 1.11429
1494 no value f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Rooted 64.4361 66.8581 1.03759
BARD1 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Squared 24787.1 27617.1 1.11417
KEAP1 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Measured 4619.81 4965.45 1.07482
PDHA1 pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Ranked 204.133 207.967 1.01878
1495 CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 1.01874
NDUFB10 nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Measured 6362.92 6838.6 1.07476
RUVBL2 ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] Squared 26974.9 30052.7 1.1141

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
- Hugo is the HGNC identifier if it exists
- 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/