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 712 to 761 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
356 splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Low confidence 202.387 194.949 1.03815
357 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] High confidence 243.12 266.661 1.09683
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Low confidence 202.387 194.949 1.03815
358 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] 207.531 199.938 1.03798
ribosomal protein l10-like protein. [refseq;acc:nm_080746] High confidence 243.12 266.662 1.09683
359 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 239.277 262.434 1.09678
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Low confidence 207.531 199.938 1.03798
360 protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] High confidence 243.072 266.559 1.09663
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Low confidence 204.231 196.773 1.0379
361 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] High confidence 242.83 266.248 1.09644
prefoldin subunit 1. [swissprot;acc:o60925] Low confidence 204.231 196.773 1.0379
362 apical-like protein (apxl protein). [swissprot;acc:q13796] High confidence 231.492 211.136 1.09641
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Low confidence 204.231 196.773 1.0379
363 choline dehydrogenase. [refseq;acc:nm_018397]
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] High confidence 231.481 211.131 1.09639
364 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Low confidence 212.235 204.495 1.03785
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] High confidence 243.208 266.617 1.09625
365 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 266.07 1.09609
sperm associated antigen 7. [refseq;acc:nm_004890] Low confidence 117.525 121.959 1.03773
366 40s ribosomal protein s5. [swissprot;acc:p46782] High confidence 242.473 265.756 1.09602
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Low confidence 207.433 199.944 1.03746
367 heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] High confidence 234.146 256.627 1.09601
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Low confidence 206.945 199.503 1.0373
368 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] 219.655 211.763 1.03727
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] High confidence 242.66 265.715 1.09501
369 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 1.09475
mad protein (max dimerizer). [swissprot;acc:q05195] Low confidence 205.943 198.554 1.03721
370 af-4 protein (proto-oncogene af4) (fel protein). [swissprot;acc:p51825] 219.597 211.722 1.0372
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] High confidence 242.159 265.104 1.09475
371 fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] Low confidence 219.599 211.723 1.0372
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] High confidence 186.52 170.42 1.09447
372 laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] Low confidence 219.598 211.722 1.0372
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] High confidence 186.52 170.42 1.09447
373 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 265.255 1.09442
all1 fused gene from 5q31. [refseq;acc:nm_014423] Low confidence 219.598 211.722 1.0372
374 excision repair protein ercc-6 (cockayne syndrome protein csb). [swissprot;acc:q03468] 210.34 202.797 1.03719
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] High confidence 267.208 244.168 1.09436
375 dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 242.686 265.516 1.09407
spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] Low confidence 219.556 211.692 1.03715
376 nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] 209.328 201.83
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] High confidence 257.017 234.945 1.09395
377 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 1.09391
l-lactate dehydrogenase a-like (ec 1.1.1.27). [swissprot;acc:q9byz2] Low confidence 205.928 198.554 1.03714
378 60s ribosomal protein l30. [swissprot;acc:p04645] High confidence 242.593 265.365 1.09387
l-lactate dehydrogenase c chain (ec 1.1.1.27) (ldh-c) (ldh testis subunit) (ldh-x). [swissprot;acc:p07864] Low confidence 205.928 198.554 1.03714
379 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] High confidence 241.509 264.163 1.0938
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Low confidence 205.928 198.554 1.03714
380 l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [swissprot;acc:p07195]
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] High confidence 242.109 264.79 1.09368
381 clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [refseq;acc:nm_015282] Low confidence 205.928 198.554 1.03714

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/