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 - 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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1458 to 1507 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
1458 EHD3 eh-domain containing protein 3. [swissprot;acc:q9nzn3] 207.024 211.086 1.01962
1459 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 192.336 188.637 1.01961
1460 TRIP12 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 205.817 209.851 1.0196
1461 RTN1 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] 207.019 211.077
1462 DLSTP dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 205.817 209.851
1463 no value pnas-18. [sptrembl;acc:q9bzu3] 161.056 164.211 1.01959
1464 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 217.351 213.18 1.01957
1465 MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]
1466 RTN2 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] 207.022 211.073
1467 MPP2 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 228.513 232.983 1.01956
1468 DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] 212.001 207.937 1.01954
1469 RTN3 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] 207.013 211.05 1.0195
1470 QARS glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 221.412 217.199 1.0194
1471 SRM spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]
1472 GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
1473 EARS2 glutamyl trna synthetase. [sptrembl;acc:o14563]
1474 RANBP5 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 218.582 214.427 1.01938
1475 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 181.882 178.438 1.0193
1476 RANBP6 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 218.591 214.457 1.01928
1477 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] 215.328 211.267 1.01922
1478 SFRS10 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
1479 MPP6 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] 228.469 232.855 1.0192
1480 CPSF6 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] 218.664 214.55 1.01918
1481 CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 208.432 204.516 1.01915
1482 LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 224.354 220.15 1.0191
1483 PDHB pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] 198.927 202.726
1484 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]
1485 RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 207.877 203.989 1.01906
1486 HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
1487 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]
1488 HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
1489 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] 213.251 209.264 1.01905
1490 PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] 221.961 226.186 1.01903
1491 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] 217.704 221.839 1.01899
1492 OPCML opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 224.159 220.017 1.01883
1493 PDHA2 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 204.146 207.988 1.01882
1494 PDHA1 pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] 204.133 207.967 1.01878
1495 CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 1.01874
1496 CSNK1A1 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]
1497 XPO1 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] 224.476 220.363 1.01866
1498 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] 224.022 219.924 1.01863
1499 DCP1A transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 224.509 220.411 1.01859
1500 COPS4 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 213.398 209.52 1.01851
1501 KIFC3 kinesin family member c3. [refseq;acc:nm_005550] 214.727 210.838 1.01845
1502 no value uridine kinase-like 1. [swissprot;acc:q9nwz5] 218.084 214.149 1.01838
1503 KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 242.181 237.834 1.01828
1504 CDC25C m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] 259.439 254.797 1.01822
1505 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] 216.158 212.316 1.0181
1506 C16orf42 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 212.103 208.339 1.01807
1507 PDK1 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 213.274 209.5 1.01801

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/