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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 575 to 624 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
red
green
network_comparison
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] no value Divided 240.758 266.078 1.10517
syntaxin 10 (syn10). [swissprot;acc:o60499] STX10 Subtracted 234.691 257.442 22.751
289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] no value Divided 272.781 246.892 1.10486
syntaxin 6. [swissprot;acc:o43752] STX6 Subtracted 234.673 257.414 22.741
290 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 Divided 231.969 210.064 1.10428
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] no value Subtracted 242.109 264.79 22.681
291 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] AK2 241.509 264.163 22.654
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] NFYB Divided 251.679 228.037 1.10368
292 40s ribosomal protein s15a. [swissprot;acc:p39027] RPS15A 241.411 266.414 1.10357
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] HNRPM Subtracted 234.146 256.627 22.481
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] no value Divided 240.782 265.717 1.10356
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 Subtracted 219.421 196.978 22.443
294 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] BCCIP Divided 240.782 265.717 1.10356
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 Subtracted 219.421 196.978 22.443
295 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 Divided 223.273 202.423 1.103
296 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2 Subtracted 219.421 196.978 22.443
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] MRPL4 Divided 241.282 266.12 1.10294
297 60s ribosomal protein l7. [swissprot;acc:p18124] no value 235.727 259.984 1.1029
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] DCPS Subtracted 219.421 196.978 22.443
298 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] CAPN2 Divided 268.632 243.588 1.10281
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] E2F1 Subtracted 266.421 244.236 22.185
299 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] CAPN1 Divided 268.635 243.592 1.10281
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Subtracted 266.421 244.236 22.185
300 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] PITRM1 Divided 150.959 166.351 1.10196
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 Subtracted 257.017 234.945 22.072
301 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 Divided 150.982 166.372 1.10193
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 Subtracted 88.2482 110.265 22.0168
302 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 Divided 242.326 267.008 1.10185
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 Subtracted 88.2482 110.265 22.0168
303 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 Divided 242.333 266.999 1.10179
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value Subtracted 88.2482 110.265 22.0168
304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Divided 242.339 266.986 1.1017
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 Subtracted 88.2482 110.265 22.0168
305 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 Divided 242.339 266.986 1.1017
306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] no value 242.153 266.673 1.10126
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted 88.2482 110.265 22.0168
307 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] MAGEA6
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR Divided 242.153 266.673 1.10126
308 60s ribosomal protein l34. [swissprot;acc:p49207] RPL34
necdin. [swissprot;acc:q99608] NDN Subtracted 88.2482 110.265 22.0168
309 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] MAGED1
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Divided 242.153 266.673 1.10126
310 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] MAGEF1 Subtracted 88.2482 110.265 22.0168
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 Divided 242.153 266.673 1.10126
311 melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B Subtracted 88.2482 110.265 22.0168
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B Divided 242.627 267.151 1.10108
312 60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L 242.195 266.663 1.10103
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value Subtracted 88.2482 110.265 22.0168

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/