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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1851 to 1900 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
463 Squared 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] 25533.3 30810.8 1.20669
Rooted rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 50.2317 55.0025 1.09498
464 Measured histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 4858.96 5568.85 1.1461
Ranked ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 226.764 1.07686
Squared homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 54726.7 45358.5 1.20654
Rooted 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] 50.2317 55.0025 1.09498
465 Measured 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] 3847.31 4409.22 1.14605
Ranked neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 248.152 267.226 1.07686
Squared trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 25310.2 30537 1.20651
Rooted 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] 50.2317 55.0025 1.09498
466 Measured transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 3847.31 4409.22 1.14605
Ranked adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 248.152 267.226 1.07686
Squared probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 25513.6 30779.5 1.2064
Rooted vav-3 protein. [swissprot;acc:q9ukw4] 66.089 72.3555 1.09482
467 Measured metastasis-associated protein mta1. [swissprot;acc:q13330] 4864.25 5573.62 1.14583
Ranked adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 248.152 267.226 1.07686
Squared nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 23531.7 28371.6 1.20568
Rooted 40s ribosomal protein s5. [swissprot;acc:p46782] 50.4649 46.1093 1.09446
468 Measured 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] 4869.15 5578.02 1.14558
Ranked leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 248.152 267.226 1.07686
Squared dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 23531.7 28371.6 1.20568
Rooted t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 107.178 117.276 1.09422
469 Measured proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 3831.17 4388.74 1.14554
Ranked fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 248.152 267.226 1.07686
Squared nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 23531.7 28371.6 1.20568
Rooted 60s ribosomal protein l9. [swissprot;acc:p32969] 51.1334 46.7335 1.09415
470 Measured block of proliferation 1. [swissprot;acc:q14137] 3796.24 4348.59 1.1455
Ranked leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 248.152 267.226 1.07686
Squared serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 10418.3 8641.84 1.20557
Rooted nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 60.0148 65.6429 1.09378
471 Measured 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] 9649.61 11053.5 1.14549
Ranked laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 248.152 267.226 1.07686
Squared phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 28188.7 33982.7 1.20554
Rooted vav-2 protein. [swissprot;acc:p52735] 66.088 72.2597 1.09339
472 Measured sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 9649.61 11053.5 1.14549
Ranked thymic stromal co-transporter. [refseq;acc:nm_033051] 248.152 267.226 1.07686
Squared gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] 28190.4 33984.1 1.20552
Rooted trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 50.3767 46.0753 1.09336
473 Measured 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] 9649.61 11053.5 1.14549
Ranked pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 225.661 209.651 1.07637
Squared beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 28190.4 33984.1 1.20552
Rooted selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 62.574 68.4128 1.09331
474 Measured rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] 9649.61 11053.5 1.14549
Ranked potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 226.789 210.818 1.07576
Squared alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 28190.4 33984.1 1.20552
Rooted flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 62.574 68.4128 1.09331
475 Measured map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 9649.61 11053.5 1.14549
Ranked potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 226.727 210.816 1.07547
Squared phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 28192 33985.3 1.20549
Rooted inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 62.574 68.4128 1.09331

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/