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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1200 to 1249 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
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] High confidence 248.463 234.095 1.06138
601 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Low confidence 208.67 202.603 1.02995
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] High confidence 206.274 218.792 1.06069
602 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Low confidence 201.426 195.579 1.0299
603 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 201.427 195.587 1.02986
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] High confidence 225.829 212.945 1.0605
604 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 1.0602
60s ribosomal protein l36. [swissprot;acc:q9y3u8] Low confidence 205.116 211.234 1.02983
605 histone h2b.c (h2b/c). [swissprot;acc:q99880] High confidence 247.47 233.441 1.0601
probable rna-dependent helicase p72 (dead-box protein p72) (dead-box protein 17). [swissprot;acc:q92841] Low confidence 204.837 198.913 1.02978
606 dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [swissprot;acc:q92685] 200.085 194.301 1.02977
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] High confidence 247.47 233.441 1.0601
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]
probable rna-dependent helicase p68 (dead-box protein p68) (dead-box protein 5). [swissprot;acc:p17844] Low confidence 204.832 198.916 1.02974
608 ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03] 205.117 211.213 1.02972
histone h2b. [refseq;acc:nm_175055] High confidence 247.47 233.441 1.0601
609 histone h2b.s (h2b/s). [swissprot;acc:p57053]
tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence 191.867 186.346 1.02963
610 histone h2b.d (h2b/d). [swissprot;acc:q99877] High confidence 247.47 233.441 1.0601
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence 191.871 186.351 1.02962
611 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] 191.875 186.357 1.02961
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] High confidence 247.47 233.441 1.0601
612 protein disulfide isomerase a4 precursor (ec 5.3.4.1) (protein erp-72) (erp72). [swissprot;acc:p13667] Low confidence 204.388 198.518 1.02957
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] High confidence 247.47 233.441 1.0601
613 histone h2b.e (h2b/e). [swissprot;acc:q99879]
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Low confidence 203.626 197.78 1.02956
614 cyclin a1. [swissprot;acc:p78396] 187.808 182.419 1.02954
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] High confidence 214.257 202.125 1.06002
615 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 1.02952
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] High confidence 214.257 202.132 1.05999
616 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
surfeit locus protein 1. [swissprot;acc:q15526] Low confidence 201.211 195.459 1.02943
617 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] 203.738 197.913
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] High confidence 214.257 202.135 1.05997
618 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Low confidence 205.472 199.6 1.02942
619 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] High confidence 214.256 202.139 1.05994
wd repeat and fyve domain containing 3 isoform 1. [refseq;acc:nm_014991] Low confidence 205.129 199.271 1.0294
620 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] High confidence 214.256 202.14 1.05994
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Low confidence 203.68 197.868 1.02937
621 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] High confidence 214.256 202.14 1.05994
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Low confidence 203.68 197.868 1.02937
622 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] High confidence 214.256 202.14 1.05994
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
623 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] High confidence 214.256 202.14 1.05994
jumonji protein. [swissprot;acc:q92833] Low confidence 207.726 201.813 1.0293
624 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] High confidence 214.256 202.139 1.05994
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] Low confidence 205.16 199.322 1.02929
625 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 203.853 198.057 1.02926

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
- 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/