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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2451 to 2500 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
613 FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted Low confidence 203.626 197.78 5.846
NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] High confidence 247.769 235.074 12.695
614 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Low confidence 201.427 195.587 5.84
CCNA1 cyclin a1. [swissprot;acc:p78396] Divided 187.808 182.419 1.02954
HOXA10 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] High confidence 214.257 202.125 1.06002
YARS tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Subtracted 232.468 245.048 12.58
615 ARPC2 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] Divided Low confidence 203.495 197.661 1.02952
HOXB9 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] High confidence 214.257 202.132 1.05999
NHP2L1 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Subtracted Low confidence 205.16 199.322 5.838
POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] High confidence 241.907 229.35 12.557
616 ARPC2 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] Low confidence 203.495 197.661 5.834
CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] High confidence 177.698 190.24 12.542
HOXA9 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Divided 214.257 202.132 1.05999
SURF1 surfeit locus protein 1. [swissprot;acc:q15526] Low confidence 201.211 195.459 1.02943
617 CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Subtracted High confidence 177.698 190.239 12.541
HOXC9 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Divided 214.257 202.135 1.05997
MEGF6 megf6 (fragment). [sptrembl;acc:o75095] Subtracted Low confidence 207.235 201.402 5.833
ZMPSTE24 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Divided 203.738 197.913 1.02943
618 CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Subtracted High confidence 177.699 190.24 12.541
GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Divided 214.256 202.139 1.05994
GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Subtracted Low confidence 204.479 198.65 5.829
SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Divided 205.472 199.6 1.02942
619 FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] High confidence 214.256 202.139 1.05994
VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Subtracted 206.274 218.792 12.518
WDFY3 wd repeat and fyve domain containing 3 isoform 1. [refseq;acc:nm_014991] Divided Low confidence 205.129 199.271 1.0294
ZMPSTE24 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Subtracted 203.738 197.913 5.825
620 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Divided 203.68 197.868 1.02937
Subtracted 5.812
GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Divided High confidence 214.256 202.14 1.05994
MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Subtracted 206.274 218.792 12.518
621 GABRA2 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Divided 214.256 202.14 1.05994
RPLP2 60s acidic ribosomal protein p2. [swissprot;acc:p05387] Subtracted 231.92 244.435 12.515
SREBF1 sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Divided Low confidence 203.68 197.868 1.02937
Subtracted 5.812
622 GABRA6 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Divided High confidence 214.256 202.14 1.05994
GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Low confidence 204.479 198.65 1.02934
RBM19 probable rna-binding protein kiaa0682. [swissprot;acc:q9y4c8] Subtracted 206.001 200.193 5.808
SYN3 synapsin iii. [swissprot;acc:o14994] High confidence 229.072 216.576 12.496
623 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Divided 214.256 202.14 1.05994
JARID2 jumonji protein. [swissprot;acc:q92833] Low confidence 207.726 201.813 1.0293
P4HB protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Subtracted 204.369 198.564 5.805
624 no value interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Divided High confidence 214.256 202.139 1.05994
HEY1 hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Subtracted 229.072 216.576 12.496
NHP2L1 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Divided Low confidence 205.16 199.322 1.02929
P4HA1 prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Subtracted 204.369 198.564 5.805
625 ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432] High confidence 229.072 216.576 12.496
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Divided Low confidence 203.853 198.057 1.02926
GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] High confidence 214.256 202.14 1.05994
P4HA2 prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Subtracted Low confidence 204.369 198.564 5.805

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/