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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3430 to 3479 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
429 PDCD6 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared Divided 29101.9 35347 1.21459
POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Ranked 239.709 259.038 1.08064
SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured 6272.91 7226.06 1.15195
430 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Squared 29098.8 35342.6 1.21457
CPE carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Subtracted 33104 38818.5 5714.5
GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Measured 6739.82 7644.63 904.81
GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Rooted 66.082 71.6526 5.5706
LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Divided 54.4927 49.6125 1.09837
LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked 227.748 210.888 1.07995
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Subtracted 250.938 234.134 16.804
TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured Divided 3804.09 4379.37 1.15123
431 BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Ranked Subtracted 233.529 216.737 16.792
CPXM1 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Squared 33104 38818.5 5714.5
DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Measured Divided 3849.94 4431.36 1.15102
FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Rooted 54.4927 49.6125 1.09837
FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Subtracted 66.082 71.6526 5.5706
GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Measured 6739.82 7644.63 904.81
SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared Divided 29096 35338.7 1.21456
TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Ranked 236.245 255.113 1.07987
432 CAPNS1 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Squared 29095.3 35337.6 1.21455
CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Subtracted 26598.9 32283.5 5684.6
ENDOG endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Ranked Divided 212.547 229.411 1.07934
GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Rooted Subtracted 66.082 71.6526 5.5706
JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Measured 6739.81 7644.62 904.81
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Rooted Divided 54.4927 49.6125 1.09837
MCTS1 mct-1 protein. [refseq;acc:nm_014060] Ranked Subtracted 226.313 243.03 16.717
PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured Divided 5244.71 6036.27 1.15093
433 AIFM1 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked 212.547 229.411 1.07934
CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared Subtracted 26598.9 32283.5 5684.6
GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Measured 6739.82 7644.62 904.8
GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Rooted 66.082 71.6526 5.5706
GCA grancalcin. [swissprot;acc:p28676] Squared Divided 29095.7 35338.3 1.21455
LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted 54.4927 49.6125 1.09837
MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Ranked Subtracted 226.313 243.03 16.717
PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Measured Divided 5244.88 6036.38 1.15091
434 no value interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Rooted Subtracted 66.082 71.6526 5.5706
CYB5R3 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Squared 26598.9 32283.5 5684.6
GABRA2 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Measured 6739.83 7644.63 904.8
NOC3L ad24 protein. [refseq;acc:nm_022451] Ranked 251.334 234.672 16.662
SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Squared Divided 18306.1 22230.6 1.21438
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted 54.4927 49.6125 1.09837
TBX6 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 229.411 1.07934
UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured 5246.38 6037.37 1.15077
435 CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Squared 26598.9 32283.5 1.21372
GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Measured Subtracted 6739.82 7644.62 904.8
JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Rooted 66.082 71.6526 5.5706
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked Divided 221.522 205.286 1.07909
PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Measured 5233.86 6022.6 1.1507
RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 50.832 46.3081 1.09769
WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Ranked Subtracted 251.299 234.729 16.57

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/