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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 2702 to 2751 of 3206 in total
expected
measured
Rank
Hugo
description
final
1.60341 0.324046 2767 no value HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] 0.202098029
1.60405 0.424703 719 ARPC5L 0.264769178
1.60594 0.448126 384 TRIP10 CDC42-INTERACTING PROTEIN 4 (THYROID RECEPTOR INTERACTING PROTEIN 10) (TRIP-10). [SWISSPROT;Acc:Q15642] 0.279042804
1.60666 0.390142 1487 no value U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 (SMALL NUCLEAR RIBONUCLEAR PROTEIN D HOMOLOG) (G7B) (SNRNP CORE SM-LIKE PROTEIN SM-X5). [SWISSPROT;Acc:Q9Y333] 0.242827979
1.60733 0.378654 1777 TATDN1 CDA11 PROTEIN. [RefSeq;Acc:NM_032026] 0.235579501
1.61155 0.353823 2392 GUK1 GUANYLATE KINASE (EC 2.7.4.8) (GMP KINASE). [SWISSPROT;Acc:Q16774] 0.219554466
1.61735 0.431627 668 FIGNL1 FIDGETIN-LIKE 1. [RefSeq;Acc:NM_022116] 0.266872971
1.61983 0.167175 3068 GNB5 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 5 (TRANSDUCIN BETA CHAIN 5). [SWISSPROT;Acc:O14775] 0.103205275
1.62441 0.427564 778 ARPC2 ARP2/3 COMPLEX 34 KDA SUBUNIT (P34-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 2). [SWISSPROT;Acc:O15144] 0.263211874
1.62535 0.407912 1105 CDA CYTIDINE DEAMINASE (EC 3.5.4.5) (CYTIDINE AMINOHYDROLASE). [SWISSPROT;Acc:P32320] 0.250968714
1.6262 0.419455 921 STUB1 STIP1 HOMOLOGY AND U-BOX CONTAINING PROTEIN 1; SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 7; CARBOXY TERMINUS OF HSP70P-INTERACTING PROTEIN; HEAT SHOCK PROTEIN A BINDING PROTEIN 2 (C-TERMINAL). [RefSeq;Acc:NM_005861] 0.257935678
1.62653 0.191363 3032 UBE2E2 0.117651073
1.62938 0.22015 2996 RNF25 RING FINGER PROTEIN 25 (EC 6.3.2.-). [SWISSPROT;Acc:Q96BH1] 0.135112742
1.63446 0.443276 535 TNPO1 IMPORTIN BETA-2 SUBUNIT (KARYOPHERIN BETA-2 SUBUNIT) (TRANSPORTIN) (M9 REGION INTERACTION PROTEIN) (MIP). [SWISSPROT;Acc:Q92973] 0.271206392
1.63455 0.412942 1070 GMCL1 0.252633447
1.63545 0.482398 313 no value BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36] 0.294963466
1.63578 0.357172 2412 N6AMT1 PUTATIVE N6-DNA-METHYLTRANSFERASE (EC 2.1.1.-) (PROTEIN PRED28) (M.HSAHEMK2P). [SWISSPROT;Acc:Q9Y5N5] 0.218349656
1.63634 0.334146 2748 WDR33 WD-REPEAT PROTEIN WDC146. [SWISSPROT;Acc:Q9C0J8] 0.204203283
2749 CPSF1 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 160 KDA SUBUNIT (CPSF 160 KDA SUBUNIT). [SWISSPROT;Acc:Q10570]"
1.63637 0.374874 2078 LHX4 LIM/HOMEOBOX PROTEIN LHX4. [SWISSPROT;Acc:Q969G2] 0.229088776
1.63914 0.392337 1629 PRKAR2A CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY CHAIN. [SWISSPROT;Acc:P13861] 0.239355394
1.63989 0.0391808 3200 RRAGA RAS-RELATED GTP BINDING A; RAS-RELATED GTP-BINDING PROTEIN. [RefSeq;Acc:NM_006570] 0.023892334
1.64277 0.366428 2262 ATP5B "ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P06576]" 0.223054962
1.64923 0.403732 1373 ARID4B 0.244800301
1.64947 0.486534 312 SNRPA1 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN A' (U2 SNRNP-A'). [SWISSPROT;Acc:P09661] 0.294963837
1.65007 0.113029 3128 MYO5B MYOSIN VB (MYOSIN 5B) (FRAGMENT). [SWISSPROT;Acc:Q9ULV0] 0.068499518
1.65321 0.38076 2025 PDHA1 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, SOMATIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE I). [SWISSPROT;Acc:P08559]" 0.230315568
1.65329 0.231971 2973 ACOT9 PUTATIVE ACYL-COA THIOESTER HYDROLASE CGI-16 (EC 3.1.2.-). [SWISSPROT;Acc:Q9Y305] 0.140308718
1.65694 0.454535 474 SIAH2 SEVEN IN ABSENTIA HOMOLOG 2. [RefSeq;Acc:NM_005067] 0.274321943
1.6585 0.427985 911 LEF1 LYMPHOID ENHANCER BINDING FACTOR 1 (LEF-1) (T CELL-SPECIFIC TRANSCRIPTION FACTOR 1-ALPHA) (TCF1-ALPHA). [SWISSPROT;Acc:Q9UJU2] 0.258055472
1.66144 0.449826 566 ELAVL1 ELAV-LIKE PROTEIN 1 (HU-ANTIGEN R) (HUR). [SWISSPROT;Acc:Q15717] 0.270744655
1.66376 0.354694 2576 YWHAZ 14-3-3 PROTEIN ZETA/DELTA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (FACTOR ACTIVATING EXOENZYME S) (FAS). [SWISSPROT;Acc:P29312] 0.2131882
1.66819 0.685868 63 FTMT MITOCHONDRIAL FERRITIN; FERRITIN HEAVY CHAIN-LIKE; FERRITIN H SUBUNIT. [RefSeq;Acc:NM_177478] 0.411145013
1.67604 0.408379 1436 U2AF2 SPLICING FACTOR U2AF 65 KDA SUBUNIT (U2 AUXILIARY FACTOR 65 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT) (HU2AF(65)). [SWISSPROT;Acc:P26368] 0.243657073
1.67671 0.408607 1432 DCLK1 SERINE/THREONINE-PROTEIN KINASE DCAMKL1 (EC 2.7.1.-) (DOUBLECORTIN- LIKE AND CAM KINASE-LIKE 1). [SWISSPROT;Acc:O15075] 0.24369569
1.6782 0.339171 2766 DDX12 DEAD/H (ASP-GLU-ALA-ASP/HIS) BOX POLYPEPTIDE 11; DEAD/H BOX-11 (CHL1-RELATED HELICASE GENE-1); YEAST CHL1 HOMOLOG. [RefSeq;Acc:NM_030655] 0.20210404
1.68007 0.410655 1390 no value 0.244427316
1.68161 0.535221 221 B9D2 0.318278911
1.6901 0.410279 1501 LIN7C LIN-7 HOMOLOG C; LIN-7 PROTEIN 3. [RefSeq;Acc:NM_018362] 0.242754275
1.69586 0.386793 2128 CSTF2 "CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA SUBUNIT). [SWISSPROT;Acc:P33240]" 0.228080738
1.69606 0.388695 2075 CSTF2T LIKELY ORTHOLOG OF MOUSE VARIANT POLYADENYLATION PROTEIN CSTF-64. [RefSeq;Acc:NM_015235] 0.229175265
1.70053 0.390544 2060 MEMO1P PROTEIN CGI-27 (C21ORF19-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y316] 0.229660165
1.7008 0.385887 2178 ADSSL1 ADENYLOSUCCINATE SYNTHASE-LIKE 1. [RefSeq;Acc:NM_152328] 0.226885583
1.70248 0.394428 1938 GUF1 0.231678493
1.70728 0.619368 109 SORBS3 VINEXIN (SH3-CONTAINING ADAPTOR MOLECULE-1) (SCAM-1). [SWISSPROT;Acc:O60504] 0.362780563
1.71147 0.460943 593 PGM2 0.269325784
1.71495 0.414708 1543 NFKBIB NF-KAPPAB INHIBITOR BETA (NF-KAPPA-BIB) (I-KAPPA-B-BETA) (IKAPPABBETA) (IKB-BETA) (IKB-B) (THYROID RECEPTOR INTERACTING PROTEIN 9) (TR- INTERACTING PROTEIN 9). [SWISSPROT;Acc:Q15653] 0.241819295
1.71705 0.415216 1542 NFKB2 NUCLEAR FACTOR NF-KAPPA-B P100/P49 SUBUNITS (H2TF1) (ONCOGENE LYT-10) (LYT10) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT]. [SWISSPROT;Acc:Q00653] 0.2418194
1.71793 0.391899 2121 LIPT1 "LIPOATE-PROTEIN LIGASE, MITOCHONDRIAL PRECURSOR (EC 6.-.-.-) (LIPOATE BIOSYNTHESIS PROTEIN) (LIPOYL LIGASE) (LIPOYLTRANSFERASE). [SWISSPROT;Acc:Q9Y234]" 0.228122799
1.71846 0.415555 1544 NFKB1 NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT (DNA-BINDING FACTOR KBF1) (EBP- 1) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT]. [SWISSPROT;Acc:P19838] 0.241818256

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/