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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green 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
red
green
network_comparison
1490 rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Subtracted 228.419 232.376 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 217.704 221.839 1.01899
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Subtracted 116.71 120.654 3.944
1492 exocyst complex component sec5. [swissprot;acc:q96kp1] 116.771 120.707 3.936
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Divided 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] 204.146 207.988 1.01882
uridine kinase-like 1. [swissprot;acc:q9nwz5] Subtracted 218.084 214.149 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] 116.845 120.772 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 204.133 207.967 1.01878
1495 casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 1.01874
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Subtracted 208.432 204.516 3.916
1496 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Divided 229.459 225.237 1.01874
kinesin family member c3. [refseq;acc:nm_005550] Subtracted 214.727 210.838 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 224.476 220.363 1.01866
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Subtracted 207.877 203.989 3.888
1498 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Divided 224.022 219.924 1.01863
1499 transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] 224.509 220.411 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 207.877 203.989 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 213.398 209.52 1.01851
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Subtracted 207.877 203.989 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] 213.398 209.52 3.878
kinesin family member c3. [refseq;acc:nm_005550] Divided 214.727 210.838 1.01845
1502 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Subtracted 219.306 223.179 3.873
uridine kinase-like 1. [swissprot;acc:q9nwz5] Divided 218.084 214.149 1.01838
1503 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 242.181 237.834 1.01828
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Subtracted 219.306 223.179 3.873
1504 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Divided 259.439 254.797 1.01822
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 219.306 223.179 3.873
1505 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Divided 216.158 212.316 1.0181
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Subtracted 219.306 223.179 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 212.103 208.339 1.01807
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Subtracted 219.306 223.179 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 213.274 209.5 1.01801
1508 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 116.524 120.375 3.851
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Divided 213.274 209.5 1.01801
1509 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 225.148 221.177 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 204.146 207.988 3.842
1510 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Divided 225.148 221.177 1.01795
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Subtracted 216.158 212.316 3.842
1511 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided 213.268 209.509 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 204.133 207.967 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] 184.656 180.823 3.833
surfeit locus protein 1. [swissprot;acc:q15526] Divided 213.268 209.509 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 187.114 190.925 3.811
1514 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Divided 213.268 209.509 1.01794
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Subtracted 198.927 202.726 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/