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 3708 to 3757 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
464 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Squared Divided 54726.7 45358.5 1.20654
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Ranked Subtracted 223.648 207.62 16.028
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Rooted 68.8237 74.1484 5.3247
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Divided 50.2317 55.0025 1.09498
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Squared Subtracted 26865.9 32332.9 5467
465 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Ranked 224.662 240.673 16.011
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided 248.152 267.226 1.07686
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Rooted Subtracted 68.8197 74.1413 5.3216
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured 2353.63 3225.65 872.02
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Rooted Divided 50.2317 55.0025 1.09498
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Squared Subtracted 26865.9 32332.9 5467
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Measured Divided 3847.31 4409.22 1.14605
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared 25310.2 30537 1.20651
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Ranked 248.152 267.226 1.07686
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured Subtracted 2353.63 3225.65 872.02
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Squared 26859 32321.2 5462.2
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked 225.661 209.651 16.01
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared Divided 25513.6 30779.5 1.2064
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted Subtracted 49.4233 54.7327 5.3094
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured Divided 3847.31 4409.22 1.14605
vav-3 protein. [swissprot;acc:q9ukw4] Rooted 66.089 72.3555 1.09482
467 40s ribosomal protein s5. [swissprot;acc:p46782] 50.4649 46.1093 1.09446
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked 248.152 267.226 1.07686
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Subtracted 248.56 232.579 15.981
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Rooted 54.9019 60.2111 5.3092
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 870.67
metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 4864.25 5573.62 1.14583
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Squared 23531.7 28371.6 1.20568
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted 25380.3 30835.9 5455.6
468 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 24832.1 30242.8 5410.7
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Rooted 54.9019 60.2111 5.3092
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Measured Divided 4869.15 5578.02 1.14558
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Squared 23531.7 28371.6 1.20568
dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] Ranked Subtracted 237.627 253.604 15.977
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Divided 248.152 267.226 1.07686
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Rooted 107.178 117.276 1.09422
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Measured Subtracted 11143.5 10276.3 867.2
469 60s ribosomal protein l9. [swissprot;acc:p32969] Rooted Divided 51.1334 46.7335 1.09415
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Ranked 248.152 267.226 1.07686
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Squared Subtracted 20988.2 15632.1 5356.1
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Divided 23531.7 28371.6 1.20568
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Ranked Subtracted 226.789 210.818 15.971
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Rooted 49.2715 54.5757 5.3042
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Measured Divided 3831.17 4388.74 1.14554
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Subtracted 11143.5 10276.3 867.2
470 block of proliferation 1. [swissprot;acc:q14137] Divided 3796.24 4348.59 1.1455
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Ranked Subtracted 224.535 240.476 15.941
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 248.152 267.226 1.07686
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Rooted Subtracted 74.8348 80.1352 5.3004
mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Squared 32174 37487.2 5313.2

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/