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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1293 to 1342 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
324 Measured DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] 28136.5 33457.6 1.18912
Ranked RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] 243.944 268.195 1.09941
Squared HARS2 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 34527.9 43507.9 1.26008
Rooted FLAD1 fad synthetase. [refseq;acc:nm_025207] 50.3803 45.4193 1.10923
325 Measured SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 16177.9 19235.4 1.18899
Ranked MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 243.944 268.195 1.09941
Squared HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] 34506.3 43476 1.25994
Rooted 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] 50.3803 45.4193 1.10923
326 Measured DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 3432.96 4081.21 1.18883
Ranked RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] 241.899 265.924 1.09932
Squared ANAPC2 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 69124.3 54897.4 1.25915
Rooted LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 50.3803 45.4193 1.10923
327 Measured SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] 16067.4 19094.4 1.18839
Ranked POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 243.817 267.962 1.09903
Squared LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 16424.1 20645.8 1.25704
Rooted 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] 50.3803 45.4193 1.10923
328 Measured BRP44 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 1.18801
Ranked DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 1.09888
Squared LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 16442.8 20662.7 1.25664
Rooted POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 50.3803 45.4193 1.10923
329 Measured SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 15999.1 19007.1 1.18801
Ranked NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 312 284 1.09859
Squared MTX2 metaxin 2. [swissprot;acc:o75431] 41236 51807 1.25635
Rooted 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] 50.3803 45.4193 1.10923
330 Measured SEPT6 septin 6. [swissprot;acc:q14141] 15959.9 18957.1 1.1878
Ranked CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 312 284 1.09859
Squared PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] 16203.4 20339.9 1.25529
Rooted SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] 50.519 45.5497 1.1091
331 Measured PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 20287.2 17083.8 1.18751
Ranked CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] 312 284 1.09859
Squared RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 33100.3 41520.6 1.25439
Rooted SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] 60.6697 67.2802 1.10896
332 Measured PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 5051.16 5975.51 1.183
Ranked NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 312 284 1.09859
Squared NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 14464.3 18142.8 1.25432
Rooted SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 60.6732 67.2827 1.10894
333 Measured PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 5039.63 5961.83 1.18299
Ranked NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 312 284 1.09859
Squared NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 14464.3 18142.8 1.25432
Rooted GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 49.0526 54.3781 1.10857
334 Measured SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 14924.4 17655.2 1.18298
Ranked NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 312 284 1.09859
Squared CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 64975.9 81151.2 1.24894
Rooted PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 58.6096 64.9655 1.10844
335 Measured DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 1.18181
Ranked CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 312 284 1.09859
Squared C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 30651.3 38253.3 1.24802
Rooted RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] 50.4705 45.5342 1.10841
336 Measured POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 3751.3 4431.34 1.18128
Ranked CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 312 284 1.09859

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/