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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2962 to 3011 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1481 CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Divided 208.432 204.516 1.01915
1482 ACTR1B beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Subtracted 225.148 221.177 3.971
LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Divided 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
RBM10 rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Subtracted 228.419 232.376 3.957
1484 CYCS cytochrome c. [swissprot;acc:p00001]
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] Divided 198.927 202.726 1.0191
1485 HS6ST2 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Subtracted 228.419 232.376 3.957
RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Divided 207.877 203.989 1.01906
1486 HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
HS6ST1 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Subtracted 228.419 232.376 3.957
1487 FA2H fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]
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] Divided 207.877 203.989 1.01906
1488 HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
WBP11 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 ELAC2 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
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] Divided 213.251 209.264 1.01905
1490 PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] 221.961 226.186 1.01903
RBM5 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 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] Divided 217.704 221.839 1.01899
PAPOLA 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 EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] 116.771 120.707 3.936
OPCML 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 no value uridine kinase-like 1. [swissprot;acc:q9nwz5] Subtracted 218.084 214.149 3.935
PDHA2 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Divided 204.146 207.988 1.01882
1494 PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Subtracted 116.845 120.772 3.927
PDHA1 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 CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Subtracted 208.432 204.516 3.916
CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] Divided 229.459 225.237 1.01874
1496 CSNK1A1 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]
KIFC3 kinesin family member c3. [refseq;acc:nm_005550] Subtracted 214.727 210.838 3.889
1497 RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 207.877 203.989 3.888
XPO1 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
1498 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] 224.022 219.924 1.01863
HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Subtracted 207.877 203.989 3.888
1499 DCP1A transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Divided 224.509 220.411 1.01859
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] Subtracted 207.877 203.989 3.888
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] Divided 213.398 209.52 1.01851
HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Subtracted 207.877 203.989 3.888
1501 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 3.878
KIFC3 kinesin family member c3. [refseq;acc:nm_005550] Divided 214.727 210.838 1.01845
1502 no value uridine kinase-like 1. [swissprot;acc:q9nwz5] 218.084 214.149 1.01838
MPI mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Subtracted 219.306 223.179 3.873
1503 no value putative ankyrin-repeat containing protein. [refseq;acc:nm_025185]
KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Divided 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
STARD3 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 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Divided 216.158 212.316 1.0181
FAT2 protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Subtracted 219.306 223.179 3.873
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] Divided 212.103 208.339 1.01807

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/