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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 575 to 624 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
575 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] DNAJB11 221.807 208.264 1.06503
576 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] no value 235.18 250.419 1.0648
577 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] PRSS7 224.606 210.944 1.06477
578 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] SF3B2
579 zinc finger protein t86. [swissprot;acc:o00488] ZNF593 246.805 231.796 1.06475
580 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] ZNRD1 236.751 252.038 1.06457
581 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] TLX3 237.28 252.492 1.06411
582 homeobox protein barh-like 1. [swissprot;acc:q9hbu1] BARX1
583 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] OPN4
584 t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] TLX2
585 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] TLX1
586 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] HECTD1
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

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/