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 expected Gene Hugo final Rank description

Results: HTML CSV LaTeX

Showing element 1001 to 1050 of 3206 in total

measured	expected	Hugo	final	Rank	description
0.0649343	0.256212	ACRC	0.25343973	1025	ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [RefSeq;Acc:NM_052957]
0.0649384	0.993221	MAGEC1	0.065381622	3150	MELANOMA-ASSOCIATED ANTIGEN C1 (MAGE-C1 ANTIGEN) (CANCER-TESTIS ANTIGEN CT7). [SWISSPROT;Acc:O60732]
0.0649797	0.993851	MAGEA6	0.065381732	3141	MELANOMA-ASSOCIATED ANTIGEN 6 (MAGE-6 ANTIGEN) (MAGE3B). [SWISSPROT;Acc:P43360]
0.0650415	0.994797	MAGEA9	0.065381681	3145	MELANOMA-ASSOCIATED ANTIGEN 9 (MAGE-9 ANTIGEN). [SWISSPROT;Acc:P43362]
0.0651212	0.285217	PUS7	0.228321594	2108
0.0651239	0.996058	no value	0.065381634	3149	MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358]
0.0651336	0.285702	HNRNPU	0.227977403	2135	HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN U (HNRNP U) (SCAFFOLD ATTACHMENT FACTOR A) (SAF-A). [SWISSPROT;Acc:Q00839]
0.0651843	0.250194	no value	0.260535025	852	KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8]
0.0652476	0.997949	MAGEA8	0.065381698	3144	MELANOMA-ASSOCIATED ANTIGEN 8 (MAGE-8 ANTIGEN). [SWISSPROT;Acc:P43361]
0.0653044	0.338193	CLSTN2	0.193098024	2832	CALSYNTENIN-2 PRECURSOR. [SWISSPROT;Acc:Q9H4D0]
0.0653411	0.271247	no value	0.240891512	1584	HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8]
0.0653467	0.286165	INTS8	0.228353223	2102
0.0653647	0.286244	GON4L	0.228353083	2103
0.0653647	0.286244	PRKCE	0.228353083	2104	"PROTEIN KINASE C, EPSILON TYPE (EC 2.7.1.-) (NPKC-EPSILON). [SWISSPROT;Acc:Q02156]"
0.0654179	0.277203	no value	0.235992756	1772	HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107]
0.0654684	0.269399	RELB	0.243016492	1469	TRANSCRIPTION FACTOR RELB (I-REL). [SWISSPROT;Acc:Q01201]
0.0654743	1.00142	MAGEB6B	0.065381458	3152	"MELANOMA ANTIGEN, FAMILY B, 6. [RefSeq;Acc:NM_173523]"
0.0654743	1.00142	NDN	0.065381458	3153	NECDIN. [SWISSPROT;Acc:Q99608]
0.0655808	0.417367	TSG101	0.157129816	2937	TUMOR SUSCEPTIBILITY GENE 101 PROTEIN. [SWISSPROT;Acc:Q99816]
0.0656049	0.159562	KIAA0430	0.411156165	51	LIMKAIN B1. [RefSeq;Acc:NM_019081]
0.0656147	1.32794	PYCRL	0.049410892	3184
0.0656459	0.270114	DEAF1	0.24303035	1464	DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG (NUCLEAR DEAF-1 RELATED TRANSCRIPTIONAL REGULATOR) (NUDR) (SUPPRESSIN) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 5). [SWISSPROT;Acc:O75398]
0.0657247	0.324347	SAPS1	0.202636991	2761
0.0658169	0.213303	SYNCRIP	0.308560592	260	NS1-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_006372]
0.0658246	1.00678	MAGEA11	0.065381315	3156	MELANOMA-ASSOCIATED ANTIGEN 11 (MAGE-11 ANTIGEN). [SWISSPROT;Acc:P43364]
0.0659071	1.00804	MAGEB18	0.065381433	3154
0.0659913	0.639469	DAB2IP	0.103197028	3072	DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552]
0.066057	0.270441	MYO7A	0.244256603	1395	MYOSIN VIIA. [SWISSPROT;Acc:Q13402]
0.0660691	0.279962	HSPA2	0.235993099	1770	HEAT SHOCK-RELATED 70 KDA PROTEIN 2 (HEAT SHOCK 70 KDA PROTEIN 2). [SWISSPROT;Acc:P54652]
0.0661338	1.0115	MAGEA10	0.065381908	3137	MELANOMA-ASSOCIATED ANTIGEN 10 (MAGE-10 ANTIGEN). [SWISSPROT;Acc:P43363]
0.0661546	0.191372	DNAJB11	0.345685889	162	DNAJ HOMOLOG SUBFAMILY B MEMBER 11 PRECURSOR (ER-ASSOCIATED DNAJ PROTEIN 3) (ERJ3) (ER-ASSOCIATED HSP40 CO-CHAPERONE) (HDJ9) (PWP1- INTERACTING PROTEIN 4). [SWISSPROT;Acc:Q9UBS4]
0.066175	1.01213	MAGEB10	0.065381917	3136
0.066175	1.01213	MAGED4	0.065381917	3135	"MELANOMA ANTIGEN, FAMILY D, 4 ISOFORM 1; MAGE1 PROTEIN; MAGE-E1 PROTEIN; MAGED4 PROTEIN. [RefSeq;Acc:NM_030801]"
0.0662042	0.380173	MAN2B1	0.174142298	2906	"LYSOSOMAL ALPHA-MANNOSIDASE PRECURSOR (EC 3.2.1.24) (MANNOSIDASE, ALPHA B) (LYSOSOMAL ACID ALPHA-MANNOSIDASE) (LAMAN) (MANNOSIDASE ALPHA CLASS 2B MEMBER 1). [SWISSPROT;Acc:O00754]"
0.0662574	1.01339	MAGED1	0.065381936	3134	MELANOMA-ASSOCIATED ANTIGEN D1 (MAGE-D1 ANTIGEN) (NEUROTROPHIN RECEPTOR-INTERACTING MAGE HOMOLOG) (PRO2292). [SWISSPROT;Acc:Q9Y5V3]
0.0662986	1.01402	TRO	0.065381945	3133	TROPHININ. [SWISSPROT;Acc:Q12816]
0.0663724	0.266132	SMAD5	0.24939654	1173	MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5 (SMAD 5) (MOTHERS AGAINST DPP HOMOLOG 5) (SMAD5) (HSMAD5) (JV5-1). [SWISSPROT;Acc:Q99717]
0.0666089	0.26852	SNTB2	0.248059362	1210	"BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]"
0.0666911	0.23892	CAPSL	0.279135694	381
0.066752	1.02096	MAGEB4	0.065381602	3151	MELANOMA-ASSOCIATED ANTIGEN B1 (MAGE-B1 ANTIGEN) (MAGE-XP ANTIGEN) (DSS-AHC CRITICAL INTERVAL MAGE SUPERFAMILY 10) (DAM10). [SWISSPROT;Acc:P43366]
0.0669169	1.02348	MAGED2	0.065381737	3140	MELANOMA-ASSOCIATED ANTIGEN D2 (MAGE-D2 ANTIGEN) (BREAST CANCER ASSOCIATED GENE 1 PROTEIN) (BCG-1) (11B6) (HEPATOCELLULAR CARCINOMA ASSOCIATED PROTEIN JCL-1). [SWISSPROT;Acc:Q9UNF1]
0.0669581	1.02411	no value	0.065381746	3138	HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932]
0.0670247	0.262934	TIMM10	0.254910738	1001	MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10. [SWISSPROT;Acc:Q9Y5J8]
0.0670488	0.303687	PGD	0.220782582	2339	"6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]"
0.0670742	0.647682	MAP1LC3B	0.103560389	3066	MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8]
0.0671204	0.252671	RPS6KA6	0.265643465	690	RIBOSOMAL PROTEIN S6 KINASE ALPHA 6 (EC 2.7.1.37) (S6K-ALPHA 6) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 6) (P90-RSK 6) (RIBOSOMAL S6 KINASE 4) (RSK-4) (PP90RSK4). [SWISSPROT;Acc:Q9UK32]
0.0671866	0.25292	no value	0.265643682	688	SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556]
0.0671887	0.24133	ZNHIT3	0.278410061	399	THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649]
0.0673124	0.302153	POLS	0.222775878	2267	POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999]
0.0673151	0.241784	NUFIP1	0.278410068	398	NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN INTERACTING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION INTERCATING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_012345]

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/