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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measured Hugo Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 2958 to 3007 of 3206 in total
measured
Hugo
Rank
description
expected
final
0.56383 NFKBIE 1547 NF-KAPPAB INHIBITOR EPSILON (NF-KAPPA-BIE) (I-KAPPA-B-EPSILON) (IKAPPABEPSILON) (IKB-EPSILON) (IKBE). [SWISSPROT;Acc:O00221] 2.33188 0.24179203
0.563839 no value 1680 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [SWISSPROT;Acc:O00232] 2.36701 0.238207274
0.565201 IRF2BP2 578 2.09213 0.270155774
0.565608 OXSM 2458 2.60988 0.21671801
0.568484 MRPL11 2198 "60S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL PRECURSOR (L11MT) (CGI-113). [SWISSPROT;Acc:Q9Y3B7]" 2.51757 0.225806631
0.570693 GLO1 2770 LACTOYLGLUTATHIONE LYASE (EC 4.4.1.5) (METHYLGLYOXALASE) (ALDOKETOMUTASE) (GLYOXALASE I) (GLX I) (KETONE-ALDEHYDE MUTASE) (S-D-LACTOYLGLUTATHIONE METHYLGLYOXAL LYASE). [SWISSPROT;Acc:Q04760] 2.83362 0.201400682
0.572386 no value 1253 IMPORTIN 4. [RefSeq;Acc:NM_024658] 2.31408 0.247349271
0.574918 HTRA1 2586 SERINE PROTEASE HTRA1 PRECURSOR (EC 3.4.21.-) (L56). [SWISSPROT;Acc:Q92743] 2.69828 0.213068325
0.574984 ATF7 587 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-7 (ACTIVATING TRANSCRIPTION FACTOR 7) (TRANSCRIPTION FACTOR ATF-A). [SWISSPROT;Acc:P17544] 2.13394 0.269447126
0.578823 SESN3 635 SESTRIN 3. [SWISSPROT;Acc:P58005] 2.15771 0.268258014
0.581959 KCTD5 1678 2.44287 0.238227577
0.582904 HDAC1 715 HISTONE DEACETYLASE 1 (HD1). [SWISSPROT;Acc:Q13547] 2.20068 0.264874493
0.584026 GORASP2 2307 "GOLGI REASSEMBLY STACKING PROTEIN 2; GOLGI REASSEMBLY STACKING PROTEIN 2, 55 KDA. [RefSeq;Acc:NM_015530]" 2.62976 0.222083384
0.584458 ATP6V0D1 1548 VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE AC39 SUBUNIT) (V-ATPASE 40 KDA ACCESSORY PROTEIN) (P39) (32 KDA ACCESSORY PROTEIN). [SWISSPROT;Acc:P12953] 2.4172 0.241791329
0.586469 KNG1 52 KININOGEN PRECURSOR (ALPHA-2-THIOL PROTEINASE INHIBITOR) [CONTAINS: BRADYKININ]. [SWISSPROT;Acc:P01042] 1.42639 0.411156135
0.587123 DYNLT1 3088 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] 6.01339 0.097635942
0.587935 RPL13A 2020 60S RIBOSOMAL PROTEIN L13A (23 KDA HIGHLY BASIC PROTEIN). [SWISSPROT;Acc:P40429] 2.55045 0.230522065
0.588043 EIF5B 1361 TRANSLATION INITIATION FACTOR IF-2. [SWISSPROT;Acc:O60841] 2.39991 0.245027105
0.588096 CIRH1A 1502 "CIRHIN; TESTIS EXPRESSED GENE 292; CIRRHOSIS, AUTOSOMAL RECESSIVE 1A. [RefSeq;Acc:NM_032830]" 2.42296 0.242717998
0.590395 CDC25C 401 M-PHASE INDUCER PHOSPHATASE 3 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25C). [SWISSPROT;Acc:P30307] 2.12136 0.278309669
0.590586 CHRAC1 6 CHROMATIN ACCESSIBILITY COMPLEX PROTEIN 1 (CHRAC-1) (CHRAC-15) (HUCHRAC15) (DNA POLYMERASE EPSILON SUBUNIT P15). [SWISSPROT;Acc:Q9NRG0] 0.969328 0.609273641
0.590899 MRPL13 2019 "60S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL (L13MT). [SWISSPROT;Acc:Q9BYD1]" 2.56327 0.230525462
RPS16 2018 40S RIBOSOMAL PROTEIN S16. [SWISSPROT;Acc:P17008]
0.593881 POLR2B 1939 DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE II SUBUNIT 2) (RPB2). [SWISSPROT;Acc:P30876] 2.5639 0.231631889
0.596138 DLD 1774 "DIHYDROLIPOAMIDE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.4) (GLYCINE CLEAVAGE SYSTEM L PROTEIN). [SWISSPROT;Acc:P09622]" 2.52689 0.23591767
0.596229 no value 1362 2.43411 0.244947435
0.59995 QKI 545 QUAKING ISOFORM 6. [SPTREMBL;Acc:Q9P0X9] 2.2133 0.271065829
0.603026 NR4A2 2775 ORPHAN NUCLEAR RECEPTOR NURR1 (IMMEDIATE-EARLY RESPONSE PROTEIN NOT) (TRANSCRIPTIONALLY INDUCIBLE NUCLEAR RECEPTOR). [SWISSPROT;Acc:P43354] 2.99447 0.201379877
0.603245 DHX15 408 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (DEAH BOX PROTEIN 15) (ATP-DEPENDENT RNA HELICASE #46). [SWISSPROT;Acc:O43143] 2.16897 0.278125101
0.604572 NACAD 254 1.93876 0.311834368
0.605547 FTHL17 64 FERRITIN HEAVY POLYPEPTIDE-LIKE 17. [SWISSPROT;Acc:Q9BXU8] 1.4734 0.410986154
0.605608 GSTZ1 2879 MALEYLACETOACETATE ISOMERASE (EC 5.2.1.2) (MAAI) (GLUTATHIONE S- TRANSFERASE ZETA 1) (EC 2.5.1.18) (GSTZ1-1). [SWISSPROT;Acc:O43708] 3.24265 0.186763295
0.607431 DLAT 2194 "DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.12) (E2) (PDC-E2) (70 KDA MITOCHONDRIAL AUTOANTIGEN OF PRIMARY BILIARY CIRRHOSIS) (PBC) (M2 ANTIGEN COMPLEX 70 KDA SUBUNIT). [SWISSPRO" 2.68753 0.226018314
0.609415 RPL11 2058 60S RIBOSOMAL PROTEIN L11. [SWISSPROT;Acc:P39026] 2.65323 0.229687965
0.61026 no value 2231 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 1) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 1) (GFAT 1) (GFAT1). [SWISSPROT;Acc:Q06210] 2.72155 0.224232515
0.617064 SIX1 666 HOMEOBOX PROTEIN SIX1 (SINE OCULIS HOMEOBOX HOMOLOG 1). [SWISSPROT;Acc:Q15475] 2.31135 0.266971251
0.61809 PDPK1 2891 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (EC 2.7.1.37) (HPDK1). [SWISSPROT;Acc:O15530] 3.46554 0.178353157
0.61918 TAF9 2669 TRANSCRIPTION INITIATION FACTOR TFIID 31 KDA SUBUNIT (TAFII-31) (TAFII-32) (TAFII32). [SWISSPROT;Acc:Q16594] 2.95928 0.209233327
0.619368 SORBS3 109 VINEXIN (SH3-CONTAINING ADAPTOR MOLECULE-1) (SCAM-1). [SWISSPROT;Acc:O60504] 1.70728 0.362780563
0.625831 no value 247 TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892] 2.00343 0.312379769
0.630538 PRKAA2 244 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-2 CHAIN (EC 2.7.1.-) (AMPK ALPHA-2 CHAIN). [SWISSPROT;Acc:P54646]" 2.01815 0.312433664
0.630724 PRPF40B 173 HUNTINGTIN INTERACTING PROTEIN C. [RefSeq;Acc:NM_012272] 1.86446 0.338287762
0.630807 ATPBD3 1736 2.66198 0.236969098
0.63284 no value 1899 60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 2.72242 0.232454948
0.634044 PPP1CA 2333 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-ALPHA 1 CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1A). [SWISSPROT;Acc:P08129] 2.86607 0.221224185
0.63619 MPHOSPH10 1563 U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN MPP10 (M PHASE PHOSPHOPROTEIN 10). [SWISSPROT;Acc:O00566] 2.6381 0.241154619
0.640883 MRPS9 2072 "28S RIBOSOMAL PROTEIN S9, MITOCHONDRIAL PRECURSOR (MRP-S9). [SWISSPROT;Acc:P82933]" 2.79379 0.229395552
0.643425 FRK 27 TYROSINE-PROTEIN KINASE FRK (EC 2.7.1.112) (NUCLEAR TYROSINE PROTEIN KINASE RAK). [SWISSPROT;Acc:P42685] 1.50997 0.426117737
0.64348 no value 2014 60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131] 2.79016 0.230624767
0.650404 MRPL4 1947 MITOCHONDRIAL RIBOSOMAL PROTEIN L4 ISOFORM A. [RefSeq;Acc:NM_015956] 2.81057 0.231413557

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/