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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1801 to 1850 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
451 no value Squared small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 17543.3 21222.5 1.20972
MRPL17 Rooted mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 50.268 45.8663 1.09597
MYCN Measured n-myc proto-oncogene protein. [swissprot;acc:p04198] 4889.71 5610.69 1.14745
POLR3C Ranked polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 239.092 257.705 1.07785
452 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 207.972 1.07784
Rooted adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 50.4595 46.0415 1.09596
SNRPF Squared small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 17543.3 21222.5 1.20972
ZNF622 Measured zinc finger-like protein 9. [refseq;acc:nm_033414] 3760.8 4315.06 1.14738
453 MED22 Rooted surfeit locus protein 5. [swissprot;acc:q15528] 50.4595 46.0413 1.09596
PPP6C Squared serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 31620.5 38250.7 1.20968
SLC45A2 Measured membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] 3760.8 4315.06 1.14738
SNRPA1 Ranked u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 224.161 207.972 1.07784
454 no value Measured guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] 3760.8 4315.06 1.14738
Ranked 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
AK3 Rooted gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 50.4595 46.0412 1.09596
SAPS3 Squared sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] 31620.5 38250.7 1.20968
455 ACACA acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 31597.8 38216.9 1.20948
GABPA Measured ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 4890.51 5610.95 1.14731
SCAPER Rooted zinc finger protein 291. [swissprot;acc:q9by12] 50.4595 46.0413 1.09596
TIMM22 Ranked mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 210.225 226.578 1.07779
456 no value Measured ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 4890.51 5610.95 1.14731
ATPAF2 Ranked atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 210.225 226.578 1.07779
NXF5 Squared nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 10933.6 13219.6 1.20908
PEX1 Rooted peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 50.4595 46.0413 1.09596
457 NDUFS8 Measured nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] 4890.51 5610.95 1.14731
NXF3 Squared nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 10936.1 13221.9 1.20901
TXNDC9 Rooted protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 50.4595 46.0413 1.09596
UQCRB Ranked ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 210.225 226.578 1.07779
458 ELOVL1 Measured elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 4890.55 5610.96 1.14731
MRPL36 Rooted 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 50.2954 45.9216 1.09524
NXF1 Squared nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 10950.4 13235.9 1.20871
SRP9 Ranked signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.922 218.925 1.07764
459 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] 233.529 216.737 1.07748
MYC Measured myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 4892.16 5611.48 1.14704
PEF1 Squared pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 27096.7 32743.5 1.20839
VAV1 Rooted vav proto-oncogene. [swissprot;acc:p15498] 66.0892 72.3741 1.0951
460 PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 50.6156 46.2239 1.09501
RRP1 Measured nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] 3790.11 4346.98 1.14693
SF3A2 Ranked splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 223.648 207.62 1.0772
TMEM189 Squared ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 29547.4 35683.5 1.20767
461 no value Rooted 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 50.6156 46.2239 1.09501
GRAP Measured grb2-related adaptor protein. [swissprot;acc:q13588] 5986.65 6865.68 1.14683
KLF5 Ranked krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] 223.648 207.62 1.0772
UGP2 Squared utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 29544.1 35678.3 1.20763
462 no value Measured ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 11383.2 9926.61 1.14674
MKI67IP Ranked mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 254.434 236.224 1.07709
RPS3 Rooted 40s ribosomal protein s3. [swissprot;acc:p23396] 50.6274 46.236 1.09498
UBE2V2 Squared ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] 29540.4 35672.6 1.20759
463 AKT1 Rooted rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 50.2317 55.0025 1.09498
ATP2C1 Squared calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 25533.3 30810.8 1.20669

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/