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 1844 to 1893 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
461 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Subtracted 0 599.896 604.911 5.015
462 leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Divided 11170.7 11305 1.01202
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 1 11383.2 9926.61 1.14674
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 2353.63 3225.65 872.02
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 0 705.758 701.071 4.687
463 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Divided 1 3720.18 4264.46 1.1463
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 0 1262.65 1248.14 1.01163
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Subtracted 1 2353.63 3225.65 872.02
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 0 146.622 150.709 4.087
464 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 23 19 4
cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1 2353.63 3225.65 872.02
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 4858.96 5568.85 1.1461
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 0 2290.09 2264.37 1.01136
465 alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 147.221 151.122 3.901
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided 6323 6254.09 1.01102
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 1 2353.63 3225.65 872.02
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] Divided 3847.31 4409.22 1.14605
466 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted 2353.63 3225.65 872.02
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Divided 0 1467.74 1483.62 1.01082
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Subtracted 793.778 796.85 3.072
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided 1 3847.31 4409.22 1.14605
467 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Subtracted 1926.69 1056.02 870.67
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 0 48 51 3
metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 1 4864.25 5573.62 1.14583
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] 0 2806.38 2782.56 1.00856
468 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] 1 4869.15 5578.02 1.14558
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Subtracted 0 48 51 3
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Divided 599.896 604.911 1.00836
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Subtracted 1 11143.5 10276.3 867.2
469 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 0 48 51 3
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Divided 1 3831.17 4388.74 1.14554
transcription factor btf3 homolog 3. [swissprot;acc:q13892] 0 219.759 221.565 1.00822
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Subtracted 1 11143.5 10276.3 867.2
470 block of proliferation 1. [swissprot;acc:q14137] Divided 3796.24 4348.59 1.1455
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 0 39165 39485 1.00817
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Subtracted 48 51 3
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 1 5367.04 6233.12 866.08
471 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 0 48 51 3
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Divided 1 9649.61 11053.5 1.14549
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Subtracted 5980.15 6843.48 863.33
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Divided 0 3855.78 3825.73 1.00785
472 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 3889.5 3919.25 1.00765
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Subtracted 48 51 3
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 1 5246.01 6109.31 863.3
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Divided 9649.61 11053.5 1.14549
473 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 0 3889.5 3919.25 1.00765
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted 48 51 3
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 1 5979.95 6842.78 862.83
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Divided 9649.61 11053.5 1.14549
474 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 0 2281.12 2263.85 1.00763

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/