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 2308 to 2357 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
577 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Rooted 121.695 131.815 1.08316
578 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Measured 6739.81 7644.62 1.13425
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Rooted 121.695 131.815 1.08316
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Squared 23534.9 27890.2 1.18506
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Ranked 224.606 210.944 1.06477
579 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Measured 6739.82 7644.62 1.13425
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Rooted 121.695 131.815 1.08316
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Squared 23526.4 27879.4 1.18503
zinc finger protein t86. [swissprot;acc:o00488] Ranked 246.805 231.796 1.06475
580 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Measured 6739.83 7644.63 1.13425
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Rooted 121.695 131.815 1.08316
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Squared 23526.4 27879.3 1.18502
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Ranked 236.751 252.038 1.06457
581 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Measured 6739.82 7644.63 1.13425
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Rooted 121.695 131.815 1.08316
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Ranked 237.28 252.492 1.06411
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Squared 23526.4 27879.3 1.18502
582 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Measured 6739.82 7644.62 1.13425
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Ranked 237.28 252.492 1.06411
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Rooted 121.695 131.815 1.08316
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Squared 23526.4 27879.3 1.18502
583 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Measured 6739.81 7644.62 1.13425
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Ranked 237.28 252.492 1.06411
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Rooted 121.695 131.815 1.08316
584 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Squared 23526.4 27879.3 1.18502
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Measured 6739.82 7644.63 1.13425
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Rooted 104.459 113.143 1.08313
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Ranked 237.28 252.492 1.06411
585 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Measured 6739.82 7644.63 1.13425
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Squared 23526.4 27879.3 1.18502
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Rooted 51.5667 55.8498 1.08306
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Ranked 237.28 252.492 1.06411
586 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] Squared 23526.4 27879.3 1.18502
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Rooted 51.5667 55.8498 1.08306
hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Ranked 237.28 252.492 1.06411
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Measured 6739.81 7644.62 1.13425
587 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Rooted 51.7204 56.0156 1.08305
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Measured 6739.83 7644.63 1.13425
homeobox protein barh-like 2. [swissprot;acc:q9umq3] Ranked 237.28 252.492 1.06411
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Squared 23526.5 27879.4 1.18502
588 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 23526.4 27879.3
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Measured 6739.83 7644.63 1.13425
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Rooted 59.7294 64.6872 1.083
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Ranked 216.557 230.362 1.06375
589 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Rooted 59.7294 64.6872 1.083
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Measured 6739.85 7644.63 1.13424
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Squared 23526.4 27879.3 1.18502
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Ranked 228.215 214.546 1.06371
590 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Squared 23526.4 27879.3 1.18502

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/