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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 536 to 585 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
red
green
network_comparison
268 Subtracted PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 241.625 265.136 23.511
269 Divided PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 241.373 267.352 1.10763
Subtracted no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 241.625 265.136 23.511
270 Divided FLAD1 fad synthetase. [refseq;acc:nm_025207] 241.373 267.352 1.10763
Subtracted RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119 23.507
271 Divided no value 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] 241.373 267.352 1.10763
Subtracted SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] 243.072 266.559 23.487
272 Divided LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 241.373 267.352 1.10763
Subtracted MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 242.83 266.248 23.418
273 Divided PAPSS1 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] 241.373 267.352 1.10763
Subtracted POLR2B dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 243.208 266.617 23.409
274 Divided POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 241.373 267.352 1.10763
Subtracted MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 266.07 23.326
275 Divided PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 241.373 267.352 1.10763
Subtracted RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] 242.473 265.756 23.283
276 Divided SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 266.969 1.10716
Subtracted DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 23.254
277 Divided no value 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 1.10665
Subtracted RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 239.277 262.434 23.157
278 Divided RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] 241.399 267.088 1.10642
Subtracted MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] 235.383 258.476 23.093
279 Divided RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 228.42 1.10605
Subtracted PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 242.66 265.715 23.055
280 Divided MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 228.356 1.10578
Subtracted TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 267.208 244.168 23.04
281 Divided no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 1.10557
Subtracted MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 22.945
282 Divided RBBP4 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] 252.39 228.297 1.10553
Subtracted NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] 242.159 265.104 22.945
283 Divided RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 1.10552
Subtracted MRPL11 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 265.255 22.885
284 Divided BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 203.235 1.10541
Subtracted POLR3A dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 242.686 265.516 22.83
285 Divided CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 224.647 203.242 1.10532
Subtracted POLR1A dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 242.691 265.481 22.79
286 Divided NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 224.633 203.251 1.1052
Subtracted RPL30 60s ribosomal protein l30. [swissprot;acc:p04645] 242.593 265.365 22.772
287 Divided RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 266.079 1.10517
Subtracted SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 225.217 202.459 22.758
288 Divided no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 266.078 1.10517
Subtracted STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] 234.691 257.442 22.751
289 Divided no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 246.892 1.10486
Subtracted STX6 syntaxin 6. [swissprot;acc:o43752] 234.673 257.414 22.741
290 Divided RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 231.969 210.064 1.10428
Subtracted no value suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 242.109 264.79 22.681
291 Divided NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 251.679 228.037 1.10368
Subtracted AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 241.509 264.163 22.654
292 Divided RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] 241.411 266.414 1.10357
Subtracted HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] 234.146 256.627 22.481
293 Divided no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 265.717 1.10356

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
- Hugo is the HGNC identifier if it exists
- 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/