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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 586 to 635 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
586 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] HECTD1 237.28 252.492 1.06411
587 homeobox protein barh-like 2. [swissprot;acc:q9umq3] BARX2
588 shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] SBDS 216.557 230.362 1.06375
589 u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] no value 228.215 214.546 1.06371
590 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] RRM1 217.215 204.279 1.06333
591 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] RPP30 216.72 230.439 1.0633
592 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] PPP1R7 91.63 97.4011 1.06298
593 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] DR1 232.118 218.406 1.06278
594 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] CDC40 223.282 210.136 1.06256
595 vav proto-oncogene. [swissprot;acc:p15498] VAV1 212.2 199.849 1.0618
596 vav-3 protein. [swissprot;acc:q9ukw4] VAV3 212.253 199.908 1.06175
597 vav-2 protein. [swissprot;acc:p52735] VAV2 212.526 200.212 1.0615
598 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] AKT1 248.463 234.095 1.06138
599 rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] AKT3
600 rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] AKT2
601 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] VPS39 206.274 218.792 1.06069
602 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] MAP4
603 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] LEF1 225.829 212.945 1.0605
604 60s ribosomal protein l15. [swissprot;acc:p39030] RPL15 217.862 230.978 1.0602
605 histone h2b.c (h2b/c). [swissprot;acc:q99880] HIST1H2BL 247.47 233.441 1.0601
606 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] HIST2H2BA
607 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] no value
608 histone h2b. [refseq;acc:nm_175055]
609 histone h2b.s (h2b/s). [swissprot;acc:p57053]
610 histone h2b.d (h2b/d). [swissprot;acc:q99877]
611 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] HIST3H3
612 testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] HIST1H2BA
613 histone h2b.e (h2b/e). [swissprot;acc:q99879] no value
614 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] HOXA10 214.257 202.125 1.06002
615 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] HOXB9 202.132 1.05999
616 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] HOXA9
617 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] HOXC9 202.135 1.05997
618 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] GABRG3 214.256 202.139 1.05994
619 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] FOXG1
620 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] GABRG1 202.14
621 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] GABRA2
622 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] GABRA6
623 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] GABRG2
624 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] no value 202.139
625 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] GABRA4 202.14
626 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] GABRE
627 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] JMJD6 202.139
628 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] GABRA1 202.14
629 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] GABRA3
630 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] NDUFA6 202.141 1.05993
631 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] PDXDC1
632 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] HOXD9 214.254 202.166 1.05979
633 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] AARS 234.106 248.104
634 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] no value 226.523 213.786 1.05958
635 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] RPL37 228.639 242.258 1.05957

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/