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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type Hugo 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
Hugo
description
red
green
network_comparison
583 Ranked OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] 237.28 252.492 1.06411
Squared AKR7A3 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 23526.4 27879.3 1.18502
Rooted HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 121.695 131.815 1.08316
584 Measured GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 6739.82 7644.63 1.13425
Ranked TLX2 t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] 237.28 252.492 1.06411
Squared ABHD3 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] 23526.4 27879.3 1.18502
Rooted SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 104.459 113.143 1.08313
585 Measured GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 6739.82 7644.63 1.13425
Ranked TLX1 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] 237.28 252.492 1.06411
Squared YIPF5 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] 23526.4 27879.3 1.18502
Rooted no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 51.5667 55.8498 1.08306
586 Measured JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 6739.81 7644.62 1.13425
Ranked HECTD1 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] 237.28 252.492 1.06411
Squared ABHD1 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 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 51.5667 55.8498 1.08306
587 Measured GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 6739.83 7644.63 1.13425
Ranked BARX2 homeobox protein barh-like 2. [swissprot;acc:q9umq3] 237.28 252.492 1.06411
Squared ALDH6A1 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] 23526.5 27879.4 1.18502
Rooted FTSJ3 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 GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 6739.83 7644.63 1.13425
Ranked SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] 216.557 230.362 1.06375
Squared HSPE1 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 23526.4 27879.3 1.18502
Rooted IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 59.7294 64.6872 1.083
589 Measured NDUFA6 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 no value 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 RABAC1 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] 23526.4 27879.3 1.18502
Rooted no value 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 PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 6739.85 7644.63 1.13424
Ranked RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 217.215 204.279 1.06333
Squared REXO2 oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] 23526.4 27879.3 1.18502
Rooted KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 108.671 100.365 1.08276
591 Measured HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 6740.5 7644.76 1.13415
Ranked RPP30 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 CHAT choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 23526.5 27879.4 1.18502
Rooted SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 108.659 100.356 1.08274
592 Measured HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] 3946.32 4475.47 1.13409
Ranked PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 91.63 97.4011 1.06298
Squared KCNAB2 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 no value 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 HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 3946.32 4475.47 1.13409
Ranked DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
Squared AKR7A2 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 23526.4 27879.3 1.18502
Rooted HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 108.653 100.352 1.08272
594 Measured 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] 3946.32 4475.47 1.13409
Ranked CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 223.282 210.136 1.06256
Squared KPNA1 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 no value 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 VAV1 vav proto-oncogene. [swissprot;acc:p15498] 212.2 199.849 1.0618
Squared PRKAA2 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
- 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/