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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Network Comparison Type Gene Value Type description Rank network_comparison Filtered Interaction Map green red
Results: HTML CSV LaTeX Showing element 368 to 417 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
green
red
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 1556 1.01656 192.996 196.192
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 980 1.03396 134.713 130.289
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 181 1.16294 267.265 229.818
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 244 1.11785 254.15 227.357
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 464 1.07686 226.764 210.578
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] 3117 1 0.00001 0.00001
ba207c16.2 (fragment). [sptrembl;acc:q9nql7] 2599 1.00142 211.361 211.662
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 2148 1.00686 219.366 217.871
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] 2115 1.007 213.14 214.632
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 931 1.03637 164.917 159.13
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 452 1.07784 207.972 224.161
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 1568 1.01646 224.767 221.128
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] 2968 1 0.00001 0.00001
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] 757 1.04968 235.583 224.434
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 2500 1.00275 219.552 218.949
bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933] 2185 1.00663 210.318 211.713
bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] 1785 1.01206 203.874 206.332
bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 459 1.07748 216.737 233.529
bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 1015 1.03236 228.906 221.73
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 651 1.05877 220.751 233.725
band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 2144 1.00688 207.864 206.443
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] 2146
band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] 2145 207.862 206.442
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 1567 1.01646 224.767 221.128
barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531] 2804 1 0.00001 0.00001
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 933 1.03635 164.951 159.165
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 2715 1.00053 215.903 216.018
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] 2950 1 0.00001 0.00001
bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745] 2776
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] 1636 1.01479 199.408 202.358
bet3 homolog. [swissprot;acc:o43617] 567 1.06563 121.261 129.219
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 1945 1.00987 222.151 224.343
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 2361 1.00415 208.046 207.186
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 301 1.10193 166.372 150.982
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 2576 1.00154 213.75 213.422
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 2578
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 50 1.26667 105 133
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 49
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] 2222 1.00637 220.108 221.509
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 2221
beta-catenin (pro2286). [swissprot;acc:p35222] 801 1.04445 214.894 224.445
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510 1.01795 221.177 225.148
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 808 1.04425 221.785 212.386
beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1] 3145 1 0.00001 0.00001
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 273 1.10763 267.352 241.373
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 271
bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 2721 1.00043 221.116 221.022
bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] 740 1.0512 235.027 223.58
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1848 1.011 216.064 218.441
biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 1711 1.01337 215.553 218.436

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/