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 601 to 650 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
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
636 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] SFRS1
637 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] PPAT
638 sorting nexin 17. [swissprot;acc:q15036] SNX17
639 nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] HRB 217.67 230.596 1.05938
640 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] no value
641 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] PRAM1
642 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] no value
643 hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] HRBL
644 cgthba protein (-14 gene protein). [swissprot;acc:q12980] C16orf35
645 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] HTATSF1
646 short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] SCOC 216.731 229.549 1.05914
647 dynein light chain 2. [refseq;acc:nm_080677] DYNLL2
648 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] MARS 218.227 206.078 1.05895
649 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] EIF4E 233.725 220.751 1.05877
650 u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] no value 228.986 216.276

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/