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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 583 to 632 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
292 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 4641.09 5588.75 1.20419
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 950.561 2108.52 1157.96
293 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided 4641.09 5588.75 1.20419
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted 4512.19 5655.52 1143.33
294 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Divided 22515.5 18702.6 1.20387
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Subtracted 4512.19 5655.52 1143.33
295 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 4577.5 1142.75
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 13261.9 11017.8 1.20368
296 nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Subtracted 3620.77 4763.34 1142.57
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Divided 4911.81 5909.18 1.20306
297 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Subtracted 3620.77 4763.34 1142.57
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Divided 4911.81 5909.18 1.20306
298 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Subtracted 8268.19 9405.85 1137.66
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Divided 4633.92 5572.85 1.20262
299 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 4914.27 5907.12 1.20203
metaxin 1. [swissprot;acc:q13505] Subtracted 9327.58 10442.2 1114.62
300 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 4446.72 5553.79 1107.07
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Divided 4914.27 5907.12 1.20203
301 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 13768.2 11466 1.20078
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Subtracted 4446.72 5553.79 1107.07
302 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided 5894.75 7073.65 1.19999
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Subtracted 6704.44 7811.45 1107.01
303 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 22268.8 18560.4 1.1998
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 4723.53 5828.46 1104.93
304 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 5221.28 6314.35 1093.07
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 4855.46 5824.52 1.19958
305 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 4624.15 1.19912
paxillin. [swissprot;acc:p49023] Subtracted 5221.28 6314.35 1093.07
306 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 8430.03 9518.11 1088.08
pnas-18. [sptrembl;acc:q9bzu3] Divided 13680.5 11409.6 1.19903
307 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Subtracted 7556.75 8636.87 1080.12
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 12365.2 14824.9 1.19892
308 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Subtracted 11852.9 10773.5 1079.4
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Divided 4977.09 5966.44 1.19878
309 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Subtracted 11848.8 10770.3 1078.5
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Divided 4977.8 5966.14 1.19855
310 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Subtracted 7551.8 8630.06 1078.26
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Divided 4909.79 5878.79 1.19736
311 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Subtracted 2820.51 3897.1 1076.59
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided 4981.52 5964.58 1.19734
312 max protein. [swissprot;acc:p25912] Subtracted 4640.26 5704.87 1064.61
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Divided 4598.21 5500.48 1.19622
313 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 21644.2 18098.7 1.1959
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Subtracted 4567.04 5631.2 1064.16
314 ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 6563.65 7627.29 1063.64
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Divided 21632.5 18090 1.19583
315 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 21370.8 17896.5 1.19413
vav proto-oncogene. [swissprot;acc:p15498] Subtracted 6644.99 7707.8 1062.81
316 serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Divided 21370.8 17896.5 1.19413
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 6603.41 7664.65 1061.24

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/