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 2958 to 3007 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1479 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Divided 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] 218.664 214.55 1.01918
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] Subtracted 213.251 209.264 3.987
1481 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 225.148 221.177 3.971
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Divided 208.432 204.516 1.01915
1482 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Subtracted 225.148 221.177 3.971
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Divided 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] 198.927 202.726
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Subtracted 228.419 232.376 3.957
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] Divided 198.927 202.726 1.0191
cytochrome c. [swissprot;acc:p00001] Subtracted 228.419 232.376 3.957
1485 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Divided 207.877 203.989 1.01906
1486 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Subtracted 228.419 232.376 3.957
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Divided 207.877 203.989 1.01906
1487 fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Subtracted 228.419 232.376 3.957
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] Divided 207.877 203.989 1.01906
1488 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Subtracted 228.419 232.376 3.957
1489 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
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] Divided 213.251 209.264 1.01905
1490 protein cgi-147. [swissprot;acc:q9y3e5] 221.961 226.186 1.01903
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

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/