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 Value Type description 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
Value Type
description
red
green
network_comparison
583 Ranked opsin 4 (melanopsin). [swissprot;acc:q9uhm6] 237.28 252.492 1.06411
Squared aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 23526.4 27879.3 1.18502
Rooted retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 121.695 131.815 1.08316
584 Measured gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 6739.82 7644.63 1.13425
Ranked t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] 237.28 252.492 1.06411
Squared alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] 23526.4 27879.3 1.18502
Rooted septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 104.459 113.143 1.08313
585 Measured gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 6739.82 7644.63 1.13425
Ranked t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] 237.28 252.492 1.06411
Squared golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] 23526.4 27879.3 1.18502
Rooted histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 51.5667 55.8498 1.08306
586 Measured phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 6739.81 7644.62 1.13425
Ranked hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] 237.28 252.492 1.06411
Squared alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] 23526.4 27879.3 1.18502
Rooted dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 51.5667 55.8498 1.08306
587 Measured gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 6739.83 7644.63 1.13425
Ranked homeobox protein barh-like 2. [swissprot;acc:q9umq3] 237.28 252.492 1.06411
Squared methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] 23526.5 27879.4 1.18502
Rooted ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 51.7204 56.0156 1.08305
588 Measured gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 6739.83 7644.63 1.13425
Ranked shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] 216.557 230.362 1.06375
Squared 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 23526.4 27879.3 1.18502
Rooted imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 59.7294 64.6872 1.083
589 Measured nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 6739.85 7644.63 1.13424
Ranked u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 228.215 214.546 1.06371
Squared rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] 23526.4 27879.3 1.18502
Rooted microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 59.7294 64.6872 1.083
590 Measured similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 6739.85 7644.63 1.13424
Ranked ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 217.215 204.279 1.06333
Squared oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] 23526.4 27879.3 1.18502
Rooted transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 108.671 100.365 1.08276
591 Measured homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 6740.5 7644.76 1.13415
Ranked ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] 216.72 230.439 1.0633
Squared choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 23526.5 27879.4 1.18502
Rooted leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 108.659 100.356 1.08274
592 Measured histone h2b.c (h2b/c). [swissprot;acc:q99880] 3946.32 4475.47 1.13409
Ranked protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 91.63 97.4011 1.06298
Squared voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] 23526.4 27879.3 1.18502
Rooted ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 108.659 100.356 1.08274
593 Measured histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 3946.32 4475.47 1.13409
Ranked tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
Squared aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 23526.4 27879.3 1.18502
Rooted transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 108.653 100.352 1.08272
594 Measured histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 3946.32 4475.47 1.13409
Ranked pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
Squared importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 23517.1 27867.3 1.18498
Rooted transforming protein n-ras. [swissprot;acc:p01111] 108.65 100.35 1.08271
595 Measured histone h2b. [refseq;acc:nm_175055] 3946.32 4475.47 1.13409
Ranked vav proto-oncogene. [swissprot;acc:p15498] 212.2 199.849 1.0618
Squared 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 34129.7 40434.8 1.18474

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/