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 Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 2980 to 3029 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1490 rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Subtracted 232.376 228.419 3.957
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] Divided 221.839 217.704 1.01899
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Subtracted 120.654 116.71 3.944
1492 exocyst complex component sec5. [swissprot;acc:q96kp1] 120.707 116.771 3.936
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Divided 220.017 224.159 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] 207.988 204.146 1.01882
uridine kinase-like 1. [swissprot;acc:q9nwz5] Subtracted 214.149 218.084 3.935
1494 poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 120.772 116.845 3.927
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Divided 207.967 204.133 1.01878
1495 casein kinase i alpha s-like. [refseq;acc:nm_145203] 225.237 229.459 1.01874
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Subtracted 204.516 208.432 3.916
1496 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Divided 225.237 229.459 1.01874
kinesin family member c3. [refseq;acc:nm_005550] Subtracted 210.838 214.727 3.889
1497 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Divided 220.363 224.476 1.01866
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Subtracted 203.989 207.877 3.888
1498 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Divided 219.924 224.022 1.01863
1499 transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 220.411 224.509 1.01859
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] Subtracted 203.989 207.877 3.888
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] Divided 209.52 213.398 1.01851
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Subtracted 203.989 207.877 3.888
1501 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] 209.52 213.398 3.878
kinesin family member c3. [refseq;acc:nm_005550] Divided 210.838 214.727 1.01845
1502 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Subtracted 223.179 219.306 3.873
uridine kinase-like 1. [swissprot;acc:q9nwz5] Divided 214.149 218.084 1.01838
1503 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 237.834 242.181 1.01828
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Subtracted 223.179 219.306 3.873
1504 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Divided 254.797 259.439 1.01822
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 223.179 219.306 3.873
1505 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Divided 212.316 216.158 1.0181
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Subtracted 223.179 219.306 3.873
1506 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Divided 208.339 212.103 1.01807
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Subtracted 223.179 219.306 3.873
1507 mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Divided 209.5 213.274 1.01801
1508 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 120.375 116.524 3.851
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Divided 209.5 213.274 1.01801
1509 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 221.177 225.148 1.01795
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Subtracted 207.988 204.146 3.842
1510 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Divided 221.177 225.148 1.01795
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Subtracted 212.316 216.158 3.842
1511 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided 209.509 213.268 1.01794
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Subtracted 207.967 204.133 3.834
1512 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 180.823 184.656 3.833
surfeit locus protein 1. [swissprot;acc:q15526] Divided 209.509 213.268 1.01794
1513 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Subtracted 190.925 187.114 3.811
1514 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Divided 209.509 213.268 1.01794
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Subtracted 202.726 198.927 3.799
1515 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]

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/