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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
461 chromodomain y-like protein 2. [refseq;acc:nm_152342] Squared 0 18606.3 18263.6 1.01876
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Measured 1915.69 1892.44 1.01229
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Rooted 62.6706 61.8357 1.0135
grb2-related adaptor protein. [swissprot;acc:q13588] Measured 1 5986.65 6865.68 1.14683
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 223.648 207.62 1.0772
scratch; scratch 1. [refseq;acc:nm_031309] 0 12164.9 12358.1 1.01588
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Squared 1 29544.1 35678.3 1.20763
462 40s ribosomal protein s3. [swissprot;acc:p23396] Rooted 50.6274 46.236 1.09498
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Ranked 0 12189.6 12378.3 1.01548
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Squared 2400.71 2356.66 1.01869
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Measured 11170.7 11305 1.01202
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Ranked 1 254.434 236.224 1.07709
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] Measured 11383.2 9926.61 1.14674
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Rooted 0 18.5298 18.2858 1.01334
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Squared 1 29540.4 35672.6 1.20759
463 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Measured 3720.18 4264.46 1.1463
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Squared 25533.3 30810.8 1.20669
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Measured 0 1262.65 1248.14 1.01163
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Ranked 5558.06 5473.99 1.01536
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Squared 2403.2 2359.13 1.01868
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Ranked 1 238.921 257.327 1.07704
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Rooted 50.2317 55.0025 1.09498
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 0 35.7784 35.3221 1.01292
464 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 30.3413 30.7252 1.01265
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Ranked 1 210.578 226.764 1.07686
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 0 10076.4 9928.08 1.01494
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Measured 1 4858.96 5568.85 1.1461
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Squared 54726.7 45358.5 1.20654
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Measured 0 2290.09 2264.37 1.01136
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Squared 18105.2 17795.2 1.01742
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] Rooted 1 50.2317 55.0025 1.09498
465 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured 0 6323 6254.09 1.01102
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Ranked 1 248.152 267.226 1.07686
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Squared 0 79185.5 77891.7 1.01661
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Rooted 48.2804 48.8876 1.01258
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] 1 50.2317 55.0025 1.09498
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 3847.31 4409.22 1.14605
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Ranked 0 9482.68 9620.66 1.01455
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared 1 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
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 0 1543 1521 1.01446
Rooted 78.4729 79.3914 1.0117
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Squared 363053 369010 1.01641
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Measured 1467.74 1483.62 1.01082
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared 1 25513.6 30779.5 1.2064
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured 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
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 0 26.5153 26.8089 1.01107

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/