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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2330 to 2379 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
583 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
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Ranked 217.215 204.279 1.06333
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Measured 6739.85 7644.63 1.13424
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Rooted 108.671 100.365 1.08276
591 choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Squared 23526.5 27879.4 1.18502
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Measured 6740.5 7644.76 1.13415
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Rooted 108.659 100.356 1.08274
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Ranked 216.72 230.439 1.0633
592 histone h2b.c (h2b/c). [swissprot;acc:q99880] Measured 3946.32 4475.47 1.13409
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Ranked 91.63 97.4011 1.06298
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Rooted 108.659 100.356 1.08274
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Squared 23526.4 27879.3 1.18502
593 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Measured 3946.32 4475.47 1.13409
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Ranked 232.118 218.406 1.06278
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted 108.653 100.352 1.08272
594 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Measured 3946.32 4475.47 1.13409
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Squared 23517.1 27867.3 1.18498
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Ranked 223.282 210.136 1.06256
transforming protein n-ras. [swissprot;acc:p01111] Rooted 108.65 100.35 1.08271
595 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 34129.7 40434.8 1.18474
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Rooted 51.2427 55.468 1.08246
histone h2b. [refseq;acc:nm_175055] Measured 3946.32 4475.47 1.13409

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/