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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Value Type Network Comparison Type Gene description Rank Filtered Interaction Map network_comparison red green
Results: HTML CSV LaTeX Showing element 368 to 417 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
red
green
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 1556 1.01656 196.192 192.996
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 130.289 134.713
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 181 1.16294 229.818 267.265
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 244 1.11785 227.357 254.15
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 464 1.07686 210.578 226.764
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] 3117 1 0.00001 0.00001
ba207c16.2 (fragment). [sptrembl;acc:q9nql7] 2599 1.00142 211.662 211.361
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 2148 1.00686 217.871 219.366
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] 2115 1.007 214.632 213.14
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 931 1.03637 159.13 164.917
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 452 1.07784 224.161 207.972
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 1568 1.01646 221.128 224.767
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 224.434 235.583
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 2500 1.00275 218.949 219.552
bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933] 2185 1.00663 211.713 210.318
bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] 1785 1.01206 206.332 203.874
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 233.529 216.737
bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 1015 1.03236 221.73 228.906
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 651 1.05877 233.725 220.751
band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 2144 1.00688 206.443 207.864
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 206.442 207.862
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 1567 1.01646 221.128 224.767
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 159.165 164.951
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 2715 1.00053 216.018 215.903
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 202.358 199.408
bet3 homolog. [swissprot;acc:o43617] 567 1.06563 129.219 121.261
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 1945 1.00987 224.343 222.151
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 207.186 208.046
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 301 1.10193 150.982 166.372
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 213.422 213.75
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 133 105
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 221.509 220.108
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 224.445 214.894
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510 1.01795 225.148 221.177
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 808 1.04425 212.386 221.785
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 241.373 267.352
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 221.022 221.116
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 223.58 235.027
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1848 1.011 218.441 216.064
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 218.436 215.553

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/