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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1462 to 1511 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
1462 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] DLSTP 205.817 209.851 1.0196
1463 pnas-18. [sptrembl;acc:q9bzu3] no value 161.056 164.211 1.01959
1464 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 217.351 213.18 1.01957
1465 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] MTO1
1466 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] RTN2 207.022 211.073
1467 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] MPP2 228.513 232.983 1.01956
1468 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] DRAP1 212.001 207.937 1.01954
1469 reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] RTN3 207.013 211.05 1.0195
1470 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] QARS 221.412 217.199 1.0194
1471 spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] SRM
1472 glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] GARS
1473 glutamyl trna synthetase. [sptrembl;acc:o14563] EARS2
1474 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] RANBP5 218.582 214.427 1.01938
1475 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] KYNU 181.882 178.438 1.0193
1476 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] RANBP6 218.591 214.457 1.01928
1477 transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] no value 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] SFRS10 215.122 211.066
1479 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] MPP6 228.469 232.855 1.0192
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] CPSF6 218.664 214.55 1.01918
1481 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] CDC23 208.432 204.516 1.01915
1482 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] LSAMP 224.354 220.15 1.0191
1483 pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] PDHB 198.927 202.726
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] TMEM91
1485 j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] RBPJ 207.877 203.989 1.01906
1486 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] HIVEP3
1487 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] HIVEP1
1488 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] HIVEP2
1489 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] MAP3K7 213.251 209.264 1.01905
1490 protein cgi-147. [swissprot;acc:q9y3e5] PTRH2 221.961 226.186 1.01903
1491 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] GPI 217.704 221.839 1.01899
1492 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] OPCML 224.159 220.017 1.01883
1493 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] PDHA2 204.146 207.988 1.01882
1494 pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] PDHA1 204.133 207.967 1.01878
1495 casein kinase i alpha s-like. [refseq;acc:nm_145203] CSNK1A1L 229.459 225.237 1.01874
1496 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] CSNK1A1
1497 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] XPO1 224.476 220.363 1.01866
1498 neurotrimin precursor (hnt). [swissprot;acc:q9p121] no value 224.022 219.924 1.01863
1499 transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] DCP1A 224.509 220.411 1.01859
1500 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] COPS4 213.398 209.52 1.01851
1501 kinesin family member c3. [refseq;acc:nm_005550] KIFC3 214.727 210.838 1.01845
1502 uridine kinase-like 1. [swissprot;acc:q9nwz5] no value 218.084 214.149 1.01838
1503 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] KRR1 242.181 237.834 1.01828
1504 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] CDC25C 259.439 254.797 1.01822
1505 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] CCDC53 216.158 212.316 1.0181
1506 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] C16orf42 212.103 208.339 1.01807
1507 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] PDK1 213.274 209.5 1.01801
1508 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] PDK2
1509 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] ACTR1A 225.148 221.177 1.01795
1510 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] ACTR1B
1511 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] COX11 213.268 209.509 1.01794

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/