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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2332 to 2381 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
583 OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Ranked 237.28 252.492 1.06411
584 ABHD3 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Squared 23526.4 27879.3 1.18502
GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Measured 6739.82 7644.63 1.13425
SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Rooted 104.459 113.143 1.08313
TLX2 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 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Rooted 51.5667 55.8498 1.08306
GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Measured 6739.82 7644.63 1.13425
TLX1 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Ranked 237.28 252.492 1.06411
YIPF5 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Squared 23526.4 27879.3 1.18502
586 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Rooted 51.5667 55.8498 1.08306
ABHD1 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
HECTD1 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Ranked 237.28 252.492 1.06411
JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Measured 6739.81 7644.62 1.13425
587 ALDH6A1 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Squared 23526.5 27879.4 1.18502
BARX2 homeobox protein barh-like 2. [swissprot;acc:q9umq3] Ranked 237.28 252.492 1.06411
FTSJ3 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
GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Measured 6739.83 7644.63 1.13425
588 GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
HSPE1 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] Squared 23526.4 27879.3 1.18502
IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Rooted 59.7294 64.6872 1.083
SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Ranked 216.557 230.362 1.06375
589 no value 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
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
NDUFA6 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
RABAC1 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Squared 23526.4 27879.3 1.18502
590 KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Rooted 108.671 100.365 1.08276
PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Measured 6739.85 7644.63 1.13424
REXO2 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Squared 23526.4 27879.3 1.18502
RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Ranked 217.215 204.279 1.06333
591 CHAT choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Squared 23526.5 27879.4 1.18502
HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Measured 6740.5 7644.76 1.13415
RPP30 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
SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Rooted 108.659 100.356 1.08274
592 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]
HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] Measured 3946.32 4475.47 1.13409
KCNAB2 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
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Ranked 91.63 97.4011 1.06298
593 AKR7A2 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Squared 23526.4 27879.3 1.18502
DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Ranked 232.118 218.406 1.06278
HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Measured 3946.32 4475.47 1.13409
HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Rooted 108.653 100.352 1.08272
594 no value 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
transforming protein n-ras. [swissprot;acc:p01111] Rooted 108.65 100.35 1.08271
CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Ranked 223.282 210.136 1.06256
KPNA1 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
595 no value histone h2b. [refseq;acc:nm_175055] Measured 3946.32 4475.47 1.13409
FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Rooted 51.2427 55.468 1.08246
PRKAA2 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
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Ranked 212.2 199.849 1.0618
596 no value cbf1 interacting corepressor. [refseq;acc:nm_004882] Rooted 60.0587 65.0057 1.08237

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/